Boris Johnson was made aware of a formal complaint about Chris Pincher's "inappropriate behaviour" while Mr Pincher was a Foreign Office minister from 2019-20, BBC News can reveal.
It triggered a disciplinary process that confirmed the MP's misconduct.
BBC News understands the PM and the foreign secretary at the time - Dominic Raab - knew about the issue.
The complaint raises fresh questions about what the PM knew before appointing the MP deputy chief whip.
The prime minister's spokesman said Mr Johnson was aware of media reports and some allegations that were "either resolved or did not progress to a formal complaint".
He added: "It was in one way concluded in some form. These issues tend to be anonymous."
Mr Pincher apologised after the process concluded, BBC News has been told, but at the time of publication the MP had not responded to our request for comment.
The MP for Tamworth was suspended as a Conservative Party MP last week over allegations he had groped two men at a private members' club in London.
He quit as Tory deputy chief whip last Thursday, but has since said he was seeking professional medical support and had no intention of resigning as an MP.
In recent days, Mr Pincher has denied a series of new allegations of inappropriate behaviour stretching back several years.
Mr Johnson appointed Mr Pincher as deputy chief whip, which involves ensuring party discipline among Tory MPs, during a cabinet reshuffle in February this year.
Mr Pincher was appointed a Foreign Office minister in July 2019 by Mr Johnson, and stayed in the post until February 2020.
During his tenure as a Foreign Office minister, an official complaint was raised about Mr Pincher for "inappropriate behaviour".
This triggered a process, overseen by the Cabinet Office, which resulted in a report that confirmed misconduct.
Both the prime minister and Deputy Prime Minister Dominic Raab, the foreign secretary at the time, were made aware of the disciplinary process, the BBC has been told.
Mr Raab's team have been approached for comment, and the Foreign Office said: "We have robust measures in place to respond to any allegations of inappropriate behaviour. It's our long-standing policy not to comment on individual cases."
The prime minister's official spokesman has previously said that before Mr Pincher was appointed a deputy chief whip, advice was sought from the government's propriety and ethics team, part of the Cabinet Office, who did not advise against the move.
On Monday evening, No 10 reiterated that the prime minister was not aware of any "specific allegations" being looked at, and that in the "absence of a formal complaint it would not be appropriate to stop the appointment".
Firefighters are tackling a "major gas explosion" in Bedford which lead to a fire "engulfing" a block of 20 flats.
Two people have been taken to hospital - one with serious injuries.
Emergency services are warning people to stay indoors and keep their windows and doors closed.
Pictures from the scene showed a three-storey block of apartments on fire, and an adjacent building has been evacuated.
A spokesperson for Bedfordshire Fire and Rescue Service said: "We are currently in attendance at a major gas explosion on Redwood Grove, Bedford.
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"There are currently six appliances, two water carriers, an incident command unit at the scene. Please avoid the area and keep windows and doors closed."
A statement from Bedfordshire Police said: "Emergency services have responded to an explosion at Redwood Grove, Bedford this morning.
"This resulted in a significant fire at a three storey block of 20 flats, which has engulfed the whole building and caused a large portion of the roof to collapse.
"There are two people who have been taken to hospital, one with serious injuries to Addenbrooke's.
"Police, fire and the ambulance service all remain in attendance."
Adam Fisher said: "A huge explosion [was] heard - everyone went to our work car park to see what was happening.
"Our building is adjacent to the apartment complex - immediately an inferno (was) visible, huge smoke cloud billowing, people screaming and people frantically calling for emergency services."
Another witness, who did not want to be named, told the PA news agency: "I walked to town and saw the flames and also witnessed someone jump from the second-floor window whilst flames were blaring out."
Protesters are targeting motorways in England, Wales and Scotland in a demonstration over high fuel prices.
Police have warned there could be "serious disruption throughout the day" as demonstrators call for a cut to fuel duty.
The action is mainly targeting three-lane motorways and is seeing convoys of vehicles driving slowly in two lanes - leaving the "fast" outside lane free.
One person has been arrested for "unsafe driving", police said.
Among the roads affected by disruption are:
the M4 and Prince of Wales Bridge
the M5 in Devon
the M32
the A38
the M180 in Lincolnshire
the A12 in Essex
the A92 in Scotland
the A64 near York
Rolling roadblocks brought parts of the M4 to a standstill with convoys travelling towards the Prince of Wales Bridge, which crosses the River Severn between England and Wales, from both directions.
The bridge was closed in the eastbound direction, while officers stopped the protest on the westbound carriageway before it reached the crossing.
But shortly before midday Gwent Police said the bridge had reopened in both directions.
Superintendent Tom Harding said the force had seen "significant delays".
Avon and Somerset Police said there had been slow-moving roadblocks on the M4, M5 and M32 but said protesters were expected to take a break before returning along the route.
Earlier, Devon and Cornwall Police said it was aware of a go-slow protest heading northbound from Exeter services of the M5.
The force also said a second protest had begun on the A38 heading north from Ivybridge, where a man in his 50s was arrested after ignoring a warning about unsafe driving.
"Unfortunately we have had unsafe driving on the A38 including vehicles travelling at a dangerously low speed," a force spokesman said.
But the force warned that journey times could be longer than normal.
In Lincolnshire police blocked junction one between the M180 and M18 forcing protesters to remain on the former, and West Yorkshire police said officers had deployed a "single tyre deflation device" - also known as a "stinger" - at the Ferrybridge services in the early stages of the protest.
The force said the device had not been used, no damage had been done to vehicles and it had since been withdrawn.
West Mercia Police said some of the tactics used during a protest on the M54, which had ended by about 08:30 BST, had "compromised the safety of other road users" and said officers would take action against those who committed traffic offences.
Fuel prices have risen to record highs in recent weeks with figures from data firm Experian showing the average price of a litre of petrol at UK forecourts had hit 191.5p and 199.0p for diesel on Sunday.
RAC fuel spokesman Simon Williams said there did not appear to be any sign of retailers reducing forecourt prices despite weekly wholesale costs having fallen for five weeks.
Gordon Balmer, executive director of the Petrol Retailers' Association, which represents independent forecourts, said rising wholesale prices were related to international events and the weakness of the pound against the US dollar.
Chancellor Rishi Sunak has said he will carefully consider calls for a "more substantial" fuel duty cut after the 5p per litre reduction implemented in March failed to halt price rises.
Rising fuel prices have been pushed even higher by the war in Ukraine, with Russia, one of the world's largest oil exporters, facing sanctions.
The government has said while it understands people are struggling with rising prices and have a right to protest, "people's day-to-day lives should not be disrupted" and warned traffic delays "will only add to fuel use".
Howard Cox, founder of campaign group FairFuelUK, said other countries had cut fuel duty more than the UK and called for a reduction of at least 20p.
While he said his organisation was not involved in the protests he said there was an appetite for them and if the government did not deliver on the issue there could be "some serious escalation of protests".
One of those taking part in the protest was Scunthorpe truck driver Tariq Akram who told the BBC his company had added £4,000 to its fuel bill in the past four months because of price rises.
He said his was one of 50 vehicles making the 60-mile journey through Scunthorpe and Doncaster at 20mph.
"The turnout was absolutely fantastic. There were 35 vehicles from our yard alone who took part," he said.
"At one point, I thought some cars wanted to overtake so I tried to let them by, then I realised they were joining in."
BBC Radio Humberside's Amanda White said when the convoy u-turned at the A15 the queues were extraordinary with "hundreds if not thousands of vehicles nose to tail crawling along".
She said while some motorists were angry others supported the protest and some even joined the convoy in their own vehicles.
Another person taking part in a protest was former HGV driver Vicky Stamper, 41, from Cwmbran, who said she and her partner had to leave their jobs in Bristol because they could not afford the fuel any longer.
"I then lost a job two weeks ago because the company couldn't afford to put fuel in that many lorries so, last in first out," she said.
Additional reporting by Jasmine Andersson.
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Sir Keir Starmer will on Monday signal that Labour is willing to fight Boris Johnson over his Brexit legacy at the next election, setting out a five-point plan to tackle the economic pain caused by Britain’s EU exit.
In a big tactical shift, Starmer will use a speech to denounce the “mess” created by the UK prime minister’s 2020 Brexit deal and the breakdown of trust with the EU caused by the row over the trading arrangements for Northern Ireland.
The Labour leader has until now shied away from talking about Brexit, fearing it would alienate Leave voters, but he has been emboldened by emerging evidence of the hit the departure has inflicted on the economy.
He will claim that Labour can “make Brexit work”, arguing that Johnson’s Brexit deal had contributed to a sense of a country that was “stuck”, with wages and growth stagnating and broken public services.
“They have created a hulking ‘fatberg’ of red tape,” he will say in a speech, comparing Brexit to the “wet wipe island” found in the river Thames. “It is hampering the flow of British business — we will break that barrier down.”
Brexit had become something of a taboo subject for Labour’s leadership: one-third of Labour supporters voted Leave in 2016 and Starmer was associated with the ill-fated campaign to overturn that result.
But new data has started to separate the economic effects of Brexit from the Covid pandemic, showing a dismal UK performance for trade and investment compared with other G7 countries.
An Ipsos UK study found last week the proportion of Britons who think Brexit has made their daily life worse has risen from 30 per cent in June 2021 to 45 per cent; only 17 per cent said their lives had been made better.
Starmer will insist that a Labour government would not seek to rejoin the EU’s single market or customs union or reintroduce freedom of movement — let alone seek to reverse the 2016 Leave vote.
“Nothing about revisiting those rows will help stimulate growth or bring down food prices or help British business thrive in the modern world — it would simply be a recipe for more division,” he will say.
Labour would seek a veterinary agreement with the EU to cut onerous agrifood checks, mutual recognition of product standards and a deal on mobility to facilitate short business trips and help artists tour in Europe.
Starmer would use the agrifood deal to remove most checks on trade between Great Britain and Northern Ireland and negotiate a trusted trader scheme to end the stand-off with Brussels over the rules, contained in the part of the Brexit deal called the Northern Ireland Protocol.
The Labour leader said business leaders wanted to safeguard the protocol, which leaves Northern Ireland in the single market for goods. “The solutions are there, the desire is there — what is lacking is trust,” he will say.
The German and Irish foreign ministers on Sunday wrote an opinion article in The Observer accusing Johnson of not engaging with Brussels on the protocol in “good faith”. They wrote there was no “legal or political justification” for his decision to introduce legislation to rip up parts of the agreement.
Starmer will say Labour would negotiate mutual recognition of professional qualifications and keep Britain in EU science programmes, including the €95bn Horizon scheme, which is cherished by UK researchers.
Data adequacy rules would be aligned but Starmer would follow Johnson in pursuing a different course on City regulation, he will say in an address to the Centre for European Reform.
The plan would also include more co-operation with the EU on justice and police matters including a new “security pact”.
Johnson is likely to portray Starmer’s speech as evidence of Labour wanting to unpick Brexit, a policy that was embraced by many working class voters in the former “red wall” in northern England.
Some senior Labour figures, including London mayor Sadiq Khan, want Starmer to go further and to commit to rejoining the EU single market, but that has been ruled out by party strategists.
Even the Liberal Democrats, who favour a return to the single market, have not set any timetable for the move, reluctant to re-engage the British public in a debate whose scars remain unhealed.
The number of people in hospital with Covid is expected to rise further, fuelling concerns about the ability to treat other illnesses, a top health official said today.
Jenny Harries, the chief executive of the UK Health Security Agency, said that the present wave of infections had not yet peaked and asked people to “go about their normal lives” but in a “precautionary way”.
Meanwhile, an organisation that represents NHS trusts said that hospital bosses were braced “for a bumpy ride” with coronavirus infections expected to add to seasonal flu pressures later this year. A heavy start to Australia’s flu season, which runs ahead of Europe’s, has been read as a potential warning sign for the UK.
Chris Pincher was "incredibly drunk" on the night he is alleged to have groped two men, MPs present at the Carlton Club that evening have told Sky News.
"He was beyond the limit when he should have been socialising," one MP claimed.
"He was slurring and mumbling some nonsense and came back in saying he needed the loo after he was asked to leave."
And asked if he had seen Mr Pincher, who has been MP for Tamworth in Staffordshire since 2010, drunk before, the MP said: "Not that bad. He was incredibly drunk."
In his first public statement since his suspension from the Tory whip, Mr Pincher, the former deputy chief whip, admitted he "drank far too much on Wednesday night" and is now seeking medical support.
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And another MP present at the Carlton Club, where Tory MPs and supporters had been attending a Conservative Friends Of Cyprus reception, told Sky News it was around 1am when Mr Pincher eventually left the club, after the bar had closed.
The latest revelations about the events in the elite club on Wednesday coincide with increasing pressure on Boris Johnson over his decision to appoint Mr Pincher to such a sensitive government post in his reshuffle in February this year.
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The Sunday Telegraph reports that the PM "turned a blind eye" to sex pest warnings about Mr Pincher.
The Sunday Mirror says he was warned twice, and The Independent claims a Conservative MP alleges he was groped twice by Mr Pincher.
The Mail on Sunday, reporting a claim first made by the PM's former chief adviser Dominic Cummings, says Mr Johnson was aware of concerns about Mr Pincher's behaviour two years ago and told aides: "He's handsy. That's a problem. Pincher by name, pincher by nature."
Downing Street did not deny that there had been concerns about Mr Pincher before his appointment, but insisted Mr Johnson "was not aware of any specific allegations".
One of the MPs present at the Carlton Club on Wednesday, asked if he was aware of Mr Pincher's reputation, told Sky News: "There have been rumours for a while, but there's a difference between rumours and hard facts."
Conservative MPs who were present praised the actions of two members of the 2019 intake, Sarah Dines and Mark Fletcher, in helping to calm things down after a man complained to Ms Dines about being groped twice by Mr Pincher.
It is understood that Ms Dines, a family law barrister who is MP for Derbyshire Dales, witnessed the incident involving one of the two men and later reported it to the government chief whip, Chris Heaton-Harris.
'She handled herself extremely well'
Describing the actions of Ms Dines in the Carlton Club, an MP who was present told Sky News: "She was trying to get Pincher to leave. She went out of her way to make the situation better. She handled herself extremely well."
When Mr Pincher did not leave, Mr Fletcher - MP for Bolsover - offered to help and took the 52-year-old former Tamworth MP outside into St James's Street in Piccadilly, but he came back in to use the lavatory before eventually leaving at around 1am, escorted by Mr Fletcher.
Pincher and Johnson powerless over by-election threat
Chris Pincher's statement breaking his silence on allegations of drunken groping was both contrite and defiant.
It was contrite because he pledged cooperation with the inquiry now being undertaken by the Commons sleaze watchdog, the Independent Complaints and Grievance Scheme.
But it was defiant because he served notice that he has no intention of quitting as an MP and hopes to return to his constituency duties "as soon as possible", he declared.
That, however, is almost certainly out of his hands. The investigation may take some time, depending on the number of complainants and witnesses.
And if the outcome is a suspension from the Commons, there is likely to be a recall petition in Tamworth which could trigger a by-election which he and Boris Johnson - after his bungled attempt to save Owen Paterson - would be powerless to prevent.
Government sources have strongly defended Ms Dines after she was criticised in The Sunday Times by one of the men accusing Mr Pincher of groping. The man said he was "taken aback" when she asked him if he was gay.
Sky News understands that Mr Heaton-Harris has confidence in her and believes she acted promptly and correctly when witnessing inappropriate behaviour and ensured the matter was reported.
'We take all allegations of this nature extremely seriously'
Describing the incident, government sources said she was approached on Wednesday by an individual who made a complaint to her about inappropriate behaviour.
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0:54
Ex-Tory MP: Double standards over Pincher
Responding to the claim that she asked if the man was gay, sources said she asked a series of questions to get a better understanding of what had happened and to establish if the individual knew Mr Pincher and if there was any prior relationship.
And it is claimed by government sources that the very fact that Ms Dines was approached about this matter and followed up on it with the chief whip shows how seriously she took it.
Responding to the latest criticism of the prime minister, a government spokesperson told Sky News: "We take all allegations of this nature extremely seriously and would encourage anyone with any allegations to come forward to the relevant authorities."
Holidaymakers are facing more travel disruption as airlines prepare to announce a new wave of cancellations next week and new strikes are planned in Spain.
Ryanair crew based in Spain plan to strike for 12 days this month to demand better working conditions, unions have said.
The announcement came on the final day of the crews' current strike, which began on Thursday and forced Ryanair to cancel 10 flights on Saturday.
It comes as Britain's busiest airport Heathrow has to tell officials about any further flight cancellations by Friday - just as some schools begin breaking up for the summer holidays, according to The Daily Telegraph.
The upheaval is in response to an amnesty announced last month that will allow airlines to cancel flights while still retaining take-off and landing slots next year.
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In other developments: • Flights were delayed at Heathrow Airport on Saturday after a technical fault with the airport's fuelling system • A technical breakdown left at least 1,500 bags stuck at Paris' Charles de Gaulle airport • A passenger travelling through Heathrow described the scene at baggage claim as looking like "a disaster movie" • The government reportedly ruled out drafting in the military to help at UK airports after Ireland put the army on standby to assist in case of further disruption at Dublin
Ryanair's next industrial action in Spain will see cabin crew strike on 12-15 July, 18-21 July and 25-28 July across the 10 Spanish airports where Ryanair operates, according to unions.
Spain-based cabin crew at easyJet are also striking for nine days this month for higher pay.
Heathrow delays
On Saturday, flights were delayed at Heathrow Airport after a technical fault with the airport's fuelling system.
The system was closed down for an hour while engineers fixed the fault.
A Heathrow spokesman told Sky News: "A technical fault with the airport's fuelling system has now been resolved.
"We are working with all airport partners to minimise disruption, however flights out of Heathrow this afternoon may be subject to delays.
"We apologise for any impact this has on people's journeys."
A passenger travelling through Heathrow described the scene at baggage claim as looking like "a disaster movie".
Adam Kent had arrived at Terminal 3 from Orlando, Florida, and said the sight "made a horrendous first impression of chaos" for international visitors.
The 59-year-old said: "(There was) lost luggage everywhere, stacked between baggage belts everyone stepping over it and no one doing anything about it.
"Being brutally honest, it looks like a serious health and safety issue.
"No one visible on the ground to explain the carnage or sort out the mess, it seems like lots of luggage has not arrived with passengers and just been dumped."
Flying is 'too cheap', says Ryanair boss
The boss of Ryanair has claimed flying has become "too cheap" and warned fares will rise for the next five years.
Michael O'Leary told the Financial Times that high oil prices and environmental charges were expected to push the average Ryanair fare up from €40 (£35) to between $50-60 (£43-£52) over the medium term.
"I find it absurd every time that I fly to Stansted, the train journey into central London is more expensive than the air fare," he told the newspaper.
Travellers have already been hit by months of cancellations, delays and missing baggage.
Staff shortages in ground handling, airports, and flight crew, have presented major challenges as the aviation sector struggles to move into the peak season after two years of coronavirus pandemic-related turbulence.
Thousands of flights have been cancelled across various airlines over recent weeks, as capacity fails to keep up with demand - a problem also being seen across Europe.
At France's Charles de Gaulle airport, airlines have been working to deliver luggage to passengers around the world after a technical breakdown left at least 1,500 bags stuck at the Paris air hub.
It comes as some airport workers are on strike in France demanding the hiring of more staff and higher wages to keep up with soaring global inflation.
The Department for Transport has temporarily relaxed rules around airport slots to help airlines avoid last-minute cancellations due to staff shortages.
It said airlines will be given a short window, described as an "amnesty", to hand back take-off and landing slots they are not confident they will be able to operate for the rest of the summer season.
It is hoped that being able to freely adjust schedules will allow airlines to run only the flights they can fully staff, ending the reports of passengers arriving at the airport to find their flights cancelled at the last minute.
On Thursday, Heathrow asked airlines to remove 30 flights from the morning peak schedule, saying that it was expecting "higher passenger numbers than the airport currently has capacity to serve".
A spokesperson for British Airways said the slot amnesty and consequent cancellations will "help us to provide the certainty our customers deserve by making it easier to consolidate some of our quieter daily flights to multi-frequency destinations well in advance".
They said that the airline "welcomes these new measures", adding: "Slot alleviation allows airlines to temporarily reduce their schedules but still retain their slots for the next year to maintain networks and provide consumers with certainty and consistency."