- Boris Johnson is facing questions about whether he tried to tone down an independent report which said Home Secretary Priti Patel broke the ministerial code by bullying staff.
Downing Street has insisted the conclusions of Sir Alex Allan's investigation were "entirely his own".
But a Whitehall source told the BBC that Sir Alex resisted pressure to make the findings more "palatable".
Ms Patel apologised yesterday, saying that her behaviour had upset people.
A source told the BBC that there were discussions between Sir Alex and Mr Johnson during the summer about challenges the report presented.
And a separate Whitehall source said Sir Alex resisted calls to downplay his findings.
Sir Alex's report found Ms Patel's conduct fell below the standards expected of government ministers.
But Mr Johnson - who has the final say - kept Ms Patel in her job and "does not believe that Priti Patel is a bully".
Sir Alex resigned as independent advisor on ministerial standards in after Mr Johnson threw his support behind the home secretary.
Labour described the allegations as "serious" and called for an independent investigation.
Holly Lynch, shadow home office minister, said: "The fact the prime minister's own adviser on standards has resigned over this issue shows how desperate the situation has become."
Downing Street said: "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."
Sir Alex, who examined Ms Patel's behaviour at three different government departments - the Home Office, Work and Pensions and International Development - found the ministerial code had been broken.
He cited examples of "shouting and swearing" and said Ms Patel's approach on occasions amounted to bullying.
In light of the findings, Ms Patel gave a "fulsome apology" and said there were "no excuses" for her conduct.
But she said she was not "supported" at the time claims were made by her department and that "issues were not pointed out to" her.
The inquiry was launched by the PM in March following the resignation of top civil servant at the Home Office, Sir Philip Rutnam.
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