Boris Johnson attempted to water down the official inquiry that found Home Secretary Priti Patel bullied staff, Whitehall sources have confirmed to Sky News.
It follows claims the prime minister tried and failed to convince his ministerial standards adviser Sir Alex Allan to tone down his finding that her behaviour amounted to bullying as he found instances of shouting and swearing.
The adviser resigned on Friday after Mr Johnson overruled his conclusion that Ms Patel breached the ministerial code and stood by his home secretary.
Offering what she described as an "unreserved, fulsome apology", Ms Patel seized on Sir Alex's finding that she received no feedback on the impact of her behaviour.
He said she was advised not to shout and swear at staff the month after her appointment in 2019 and that he told her to treat staff with respect "on a number of further occasions".
Sir Philip also said he was not interviewed for the inquiry despite him having launched a constructive dismissal claim at an employment tribunal.
Sir David Omand, a former permanent secretary at the Home Office, told Sky News the controversy indicated "a gradual erosion of standards in public life".
He said the PM had "got himself in a completely unnecessary problem by rejecting the advice of his independent adviser because he doesn't like it".
"Well, that's not a very good reason for rejecting a very well-reasoned report," Sir David added.
"It's a rather adversarial approach and we saw that with his former adviser Dominic Cummings' comments.
"It's starting out from a position of 'I can't trust these officials' which is exactly the wrong position to start with.
"It's very much like President Trump's book The Art Of The Deal: you try and sort of bully your opponent into agreeing a deal, and that may work in real estate but it doesn't work when you're negotiating on behalf of the country or reaching long-term agreements on behalf of the country."
Speaking to Sky News, former diplomat and national security adviser Lord Ricketts said Sir Alex must have felt his position was "untenable" after being overridden by Mr Johnson.
He said: "The ministerial code is policed by the prime minister and if the prime minister rejects the finding of his independent adviser then there is clearly something quite wrong with the situation.
"It seems to imply that bullying by a senior minister is acceptable and that sends a very bad signal for relations between ministers and the civil service."
He added: "The country is facing such a serious issue with recovery from the pandemic, we need ministers and civil servants to be working together confidently, with trust and with frankness on both sides and this episode has not helped that."
Downing Street has not denied reports that Mr Johnson tried to influence the report's findings, with a spokesman instead saying: "As you would expect, the prime minister spoke to Sir Alex Allan to further his understanding of the report.
"Sir Alex's conclusions are entirely his own."
Labour has called for an urgent investigation and called for the "initial, unedited report" to be published in full.
Shadow home office minister Holly Lynch said: "These are serious allegations that suggest Boris Johnson tried to interfere with an investigation into bullying accusations against one of his closest political allies."
However, Number 10 has indicated the full report into Ms Patel's conduct would not be published in order to protect those who gave evidence.
The chairman of the Committee on Standards in Public Life, Lord Evans of Weardale, said Sir Alex's resignation was "deeply concerning" and that his committee would look "urgently" at what had happened as part of its review of the ministerial code.