Rishi Sunak is facing scrutiny over whether he knew about Gavin Williamson’s alleged bullying of a senior civil servant whom he told to “cut your throat” before reappointing him to government. Two sources claimed the prime minister had been alerted to Williamson’s “credible and substantiated bad behaviour” while defence secretary when he drew up his cabinet. One of them said Sunak was given a “general description” of the alleged bullying incident at the Ministry of Defence but gave Williamson a job regardless. However, Downing Street has strongly rejected the claims that the Sunak and the cabinet secretary, Simon Case, knew of the bullying allegations before they were reported by the Guardian. A government spokesperson said: “All the allegations made in this story are categorically untrue.” At prime minister’s questions, Sunak conceded that he regretted bringing Williamson back into the cabinet as he faced questions over his judgment, but insisted he was unaware of “any of the specific concerns” relating to Williamson’s time in previous roles. He told MPs: “I obviously regret appointing someone who has had to resign in the circumstances. But I think what the British people would like to know is that when situations like this arise, that they will be dealt with properly. “That’s why it is absolutely right that he resigned and it’s why it is absolutely right that there is an investigation to look into these matters properly.” Williamson resigned from the cabinet on Tuesday after the Guardian revealed claims that while he was defence secretary he told a former senior civil servant to “slit your throat”. Williamson said the claims had become a “distraction” for the government and he wanted to clear his name. It followed allegations he sent expletive-laden messages to the former Conservative chief whip Wendy Morton complaining about not being invited to the Queen’s funeral. The former deputy chief whip Anne Milton alleged that Williamson used “unethical and immoral” methods while he was in charge of party discipline as chief whip. She told Channel 4: “I think he feels that he’s Francis Urquhart from House of Cards.” Another former colleague told the Guardian they recalled Williamson being “spectacularly rude” to civil servants who were giving him a presentation. He is now subject to three separate investigations into his behaviour – two by parliament’s independent complaints and grievances service, and one internal Conservative party investigation. Keir Starmer accused Sunak of being unable to stand up to “a cartoon bully with a pet spider” as he condemned him for having appointed Williamson – who as Theresa May’s chief whip kept a pet tarantula in his office as part of a calculated image of menace – and then expressing “great sadness” at his departure. “Everyone in the country knows someone like [Williamson], a sad middle manager getting off on intimidating those beneath it,” the Labour leader said at PMQs. “But everyone in the country also know someone like the prime minister, the boss who is so weak, so worried the bullies will turn on him, that he hides behind them.” Williamson’s resignation prompted fresh doubts among some Conservative MPs about Sunak’s political judgment, after he faced questions for reappointing Suella Braverman as home secretary after she was forced out for breaking the ministerial code. The Guardian has been told that Case and his team informally briefed Sunak, as is standard practice, on any potential risks associated with ministerial appointments. One well-placed Whitehall insider claimed Case gave the prime minister a “general description, rather than the exact wording”, of the MoD incident. Another source said the PM was told of Williamson’s reputation for “gathering and using kompromat” and “violent and vulgar language” when speaking to aides and MPs, as well as being “irresponsible” with secure information. Allies of Sunak suggested the Cabinet Office had no record of even the generalities of the MoD incident. However, the Guardian has been told that Stephen Lovegrove, then permanent secretary of the Ministry of Defence, was aware of the specific allegation of Williamson having bullied a senior civil servant and was believed to have passed this on to the Cabinet Office. One senior Tory source confirmed that Lovegrove had informed both the political side of the No 10 operation and then Mark Sedwill, Case’s predecessor as cabinet secretary, that there had been an informal complaint about Williamson – but told them the MoD wanted to deal with it internally. “We were made aware of problems with how Gavin was behaving towards civil servants in the department. It was the cabinet secretary’s responsibility to make the propriety and ethics team aware,” they said. Williamson is a divisive figure at Westminster, where he is viewed with suspicion by many Tory MPs because of his reputation as an inveterate plotter. Downing Street said the MP, who has previously been sacked as defence secretary and education secretary, offered his resignation to Sunak in a face-to-face meeting on Tuesday night.