Gavin Williamson dramatically quit Rishi Sunak’s cabinet on Tuesday night after the Guardian revealed claims that he told a senior civil servant they should “slit your throat” while he was defence secretary. The Cabinet Office minister stepped down after the former Whitehall aide put in a formal complaint to parliament’s Independent Complaints and Grievance Scheme (ICGS), piling more pressure on Sunak over his decision to reappoint his ally. Williamson’s fate appeared to be sealed after further bullying allegations from his former deputy chief whip, who criticised his “unethical and immoral” behaviour and claimed he used “leverage” and threats to control MPs and instil a culture of fear in Westminster. In his resignation letter, the MP conceded that claims about his conduct had become a “distraction” and he had decided to “step back from government” while the complaints process was carried out, vowing to “clear my name of any wrongdoing”. In his response, Sunak said he was accepting Williamson’s resignation with “great sadness” but added that he supported his decision to stand down. The prime minister also thanked his political ally for his “personal support and loyalty” and the work he had done during his brief spell in government. His decision to quit – the third time he has been forced to leave cabinet after he was sacked as defence secretary by Theresa May and education secretary by Boris Johnson – follows allegations he sent expletive-laden messages to former chief whip Wendy Morton complaining about not being invited to the queen’s funeral. However, the manner of his departure – stepping down rather than being forced out by the prime minister – will raise further questions about Sunak’s political judgment, with his controversial cabinet appointments, also including the home secretary, Suella Braverman, overshadowing his first few weeks in office. The Conservative whip’s office confirmed that the former minister remained a Tory MP for now, with a spokesperson saying: “Sir Gavin Williamson has been clear that he will comply with the ongoing complaints process. It is right that we wait for that process to conclude.” Williamson is now facing three separate inquiries into his behaviour, two with the ICGS and the other an internal Conservative party investigation. Two relate to the same incident involving Morton. The third follows the revelations in the Guardian that Williamson allegedly told a senior civil servant to “slit your throat” and “jump out of the window”, in what they claimed was a bullying campaign while he was defence secretary. Williamson has rejected the allegations that he bullied any staff, claiming to have had “good working relationships” with his “brilliant officials”, but has not denied using the specific words. In a statement, the complainant said they had an “incredibly difficult period” working for Williamson at the MoD and that the alleged bullying had taken “an extreme impact” on their mental health. In a separate development, two further sources who spoke to the Guardian claimed that during his time as chief whip Williamson had been heard joking or boasting about the effect his tactics had on the mental health of those he worked with, with one saying it had “made people uncomfortable”. In an extraordinary interview with Channel 4 News, Anne Milton accused Williamson of using MPs’ mental and physical health problems against them, collecting “salacious gossip” about their “sexual preferences” and on one occasion telling her to give an MP with financial problems a cheque and tell them: “I now own him.” According to Milton, who stepped down as an MP in 2019, the former chief whip sent her an email in response to a female civil servant’s inquiry about why a minister had to change travel plans to attend a vote, saying: “Always tell them to fuck off and if they have the bollocks to come and see me. Fuck jumped up civil servants.” She added: “It’s an image he cultivates. I think he feels that he’s Francis Urquhart from House of Cards.” Downing Street had said Sunak believed that the MoD bullying allegations against Williamson were serious, and was considering whether further action should be taken against him. It has not yet responded to the allegations in the Channel 4 interview. The prime minister’s official spokesperson had signalled that Sunak might not wait for formal investigations to fully complete before deciding what, if any, action to take. Before the latest claims, he said that Sunak retained full confidence in the Cabinet Office minister and believed his denial. However, in a statement the complainant said: “I have made the decision to formally report Gavin Williamson’s behaviour while at the Ministry of Defence to parliament’s Independent Complaints and Grievance Scheme. “This was an incredibly difficult period for me. Gavin Williamson’s words and actions had an extreme impact on my mental health. Government ministers have a code of conduct that they are required to follow. Any form of abuse is unacceptable. “I have decided to come forward after feeling stronger given the passage of time and after seeing the nature of his messages to Wendy Morton.” The latest investigation comes after Morton said Williamson had sent her offensive WhatsApp messages because he was upset he had not been invited to the Queen’s funeral. The Guardian understands he has still not apologised to the Tory MP despite saying he had done so. In his resignation letter to the prime minister, Williamson said there was an ongoing complaints process “concerning text messages I sent to a colleague”. He added: “I am complying with this process and I have apologised to the recipient for those messages.” “Since then, there have been other allegations made about my past conduct. I refute the characterisation of these claims, but I recognise these are becoming a distraction for the good work this government is doing for the British people. “I have therefore decided to step back from government so that I can comply fully with the complaints process that is under way and clear my name of any wrongdoing.” Williamson would be entitled to about £16,876 in severance pay for lasting exactly two weeks in government, in addition to £2,589 in gross pay, but he tweeted on Tuesday night that he would not be taking it. “This is taxpayers’ money and it should go instead toward the government‘s priorities like reducing the NHS’s waiting lists,” he said. The Labour deputy leader, Angela Rayner, said: “This is a damning reflection of a weak prime minister. Rishi Sunak appointed Gavin Williamson with full knowledge of serious allegations about his conduct and repeatedly expressed confidence in him. “This is yet another example of Rishi Sunak’s poor judgment and weak leadership. It is clear that he is trapped by the grubby backroom deals he made to dodge a vote, and is incapable of putting country before party. “As families struggle during a cost of living crisis made in Downing Street, yet another Tory government has descended into chaos.”