Sir Gavin Williamson has resigned as a minister in the UK government, saying allegations about his behaviour were “becoming a distraction for the good work this government is doing”.

The announcement came as he was facing a series of inquiries into his “unethical and immoral” conduct.

Accepting Sir Gavin Williamson’s resignation “with great sadness”, Prime Minister Rishi Sunak said: “I would like to thank you for your personal support and loyalty.”

No 10 is carrying out a fact-finding exercise following claims that the Cabinet Office minister told a senior civil servant he would “slit your throat”, and as the Tory party and Parliament’s bullying watchdog are looking into allegations made by former chief whip Wendy Morton.

Pressure mounted on Sir Gavin when his former deputy Anne Milton alleged he used intimidatory and threatening tactics while he was chief whip.

Addressing an accusation made against Sir Gavin by Ms Milton that suggested he had “used people's mental health against them,” Education Secretary Gillian Keegan told Sky News on Wednesday: “These are allegations he is obviously denying.

“It’s inappropriate to use anybody’s mental health against them. Obviously he has denied the allegations and he has said he doesn’t want to be a distraction and he’s going to repute them from the backbenches via the independent process.

“Mental health is very serious.”

David Lammy, shadow foreign secretary, told BBC Radio 4's Today Programme on Wednesday that Sir Gavin's behaviour was “repellent, odious and unacceptable”.

“He appointed him as some sort of enforcer — apparently because this is the way he behaves,” he said.

“We really should have an account of why he came back into government. It's not clear in the first place why this individual was knighted for services to this country.”

The former defence secretary has been reported in formal complaints to Parliament’s Independent Complaints and Grievance Scheme (ICGS).

Mr Sunak’s decision to give a Cabinet-level role to the twice-sacked minister has led critics to question his judgment.

No 10 had said on Tuesday that Mr Sunak still maintained confidence in his ally, but indicated the prime minister would act if necessary.

In the latest disclosures, Ms Milton accused Sir Gavin of seeking to use an MP’s financial difficulties as leverage against them and sending an expletive-laden email about a female civil servant.

Ms Milton, who was deputy chief whip from May 2015 to June 2017, described his behaviour as “unethical and immoral”, claiming: “I think he feels that he’s [the character] Francis Urquhart from House Of Cards.”

Stripped of the Tory whip position during the Brexit rows in 2019 and subsequently losing her seat, Ms Milton told Channel 4 News: “I got the impression that he loved salacious gossip and would use it as leverage against MPs if the need arose.”

She told the broadcaster that Sir Gavin had ranted about civil servants in 2016 in response to a female official asking why a minister had to change travel plans for a vote.

Ms Milton said that when the whips’ office gave some financial assistance to an MP, Sir Gavin told her that when she handed over the cheque she should make sure “he knows I now own him”.

She questioned Mr Sunak’s decision to give Sir Gavin a ministerial job, saying: “I think [at] best it was probably a bit naive. I don’t know that there are many people that would hang out the bunting to see Gavin Williamson back in government.”

The claims by Ms Milton follow allegations that Sir Gavin clashed with a civil servant while he was defence secretary.

Sir Gavin denied the official’s allegation of a campaign of bullying but did not deny making the remarks, including telling the civil servant to “jump out of the window”.

“Those are serious allegations that have come in,” said the prime minister’s official spokesman.

In a statement following reports, Sir Gavin said: “I strongly reject this allegation and have enjoyed good working relationships with the many brilliant officials I have worked with across government.”

The PA news agency understands that former chief whip Ms Morton has referred her complaint to Parliament’s bullying watchdog, while an internal Tory party inquiry is ongoing.

Sir Gavin’s ministerial responsibilities included the Geospatial Commission, the Government Communications Service and the “Great Campaign” to promote the UK.

“After a week of appalling allegations about intimidatory behaviour towards colleagues, the prime minister has rewarded Williamson by giving him authority over huge swathes of the civil service,” deputy Labour leader Angela Rayner said.

The prime minister has been criticised for his decision to bring his ally back into government despite knowing about the complaint made by Ms Morton.

The Times, which first disclosed that she has referred her complaint to Parliament’s ICGS, said she made the move over fears of a “whitewash” by the Conservative Party.

In a series of texts peppered with swear words, Sir Gavin accused Ms Morton of seeking to “punish” MPs out of favour with Liz Truss who was prime minister at the time by excluding them from Queen Elizabeth II’s funeral, warning: “There is a price for everything.”

The Liberal Democrats demanded an independent inquiry into Sir Gavin’s conduct so the Tories do not “mark their own homework”.

Sir Gavin, who was knighted after being nominated for the honour by Boris Johnson earlier this year, is a divisive figure at Westminster, where he is viewed with suspicion by many Tory MPs because of his reputation as an inveterate plotter.

He was sacked first by former prime minister Theresa May as defence secretary in 2019 for leaking details of a National Security Council meeting, and then by Mr Johnson as education secretary over the Covid-19 A-levels debacle.

However, he was regarded as a key figure in Mr Sunak’s campaign over the summer to become party leader.