Boris Johnson is facing questions regarding the official inquiry that found Home Secretary Priti Patel bullied staff amid allegations he tried to pressure his standards advisor to water it down.

Downing Street did not deny suggestions that Mr Johnson had tried and failed to convince Sir Alex Allan to tone down his conclusion insisting that the conclusions of Sir Alex Allan's investigation were "entirely his own".

The adviser quit on Friday when the Prime Minister 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.

But Sir Philip Rutnam, who quit as the Home Office’s permanent secretary after accusing Ms Patel of a “vicious and orchestrated briefing campaign” against him, contested this.

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.

Meanwhile, the Times reported two unnamed senior Whitehall officials saying that the Prime Minister tried and failed to get Sir Alex to tone down his report to find there was no clear evidence of bullying.

READ MORE: Standards investigator resigns after PM over-rules him and insists Priti Patel did not break ministerial code

Sir Alex AllanSir Alex Allan has resigned as Boris Johnson’s adviser on ministerial standards (PA)

Downing Street did not deny the report, with a No 10 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.”

Shadow home office minister Holly Lynch said the “initial, unedited report” must be published in full and called for an independent investigation.

“These are serious allegations that suggest Boris Johnson tried to interfere with an investigation into bullying accusations against one of his closest political allies,” the Labour MP said.

Sir Alex found Ms Patel had not always treated civil servants with “consideration and respect” and concluded that her approach on occasions “amounted to behaviour that can be described as bullying in terms of the impact felt by individuals”.

He said Ms Patel had “not consistently met the high standards required by the ministerial code”, though he said there was “no evidence that she was aware of the impact of her behaviour”.

The Home Secretary apologised and said there were “no excuses” for what happened but highlighted Sir Alex’s assessment of her awareness.

She told the BBC that “any upset that I’ve caused is completely unintentional and at the time, of course it says it’s in the report, that issues were not pointed out to me”.

Later on, Sir Philip released a statement through the FDA union for civil servants saying that he was “at no stage asked to contribute evidence” to the investigation.

“The advice states that no feedback was given to the Home Secretary and that she was therefore unaware of issues that she might otherwise have addressed. This is not correct,” he said.

READ MORE: Labour demands full and immediate publication of Patel report, saying probe has 'all hallmarks of a cover-up'

“As early as August 2019, the month after her appointment, she was advised that she must not shout and swear at staff.

“I advised her on a number of further occasions between September 2019 and February 2020 about the need to treat staff with respect and to make changes to protect health, safety and wellbeing.”

Mr Johnson, who is the ultimate arbiter of the ministerial code, judged that Ms Patel did not breach the rules and continues to have “full confidence in her” and “considers this matter now closed”.

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.

Mr Johnson’s press secretary Allegra Stratton said: “The Prime Minister does personally take these allegations exceedingly seriously. He loathes bullying.

“He did say that he would not tolerate bullying. He hasn’t tolerated bullying. It is not his belief that Priti Patel is a bully.”

Downing Street indicated that the full report into Ms Patel’s conduct would not be published in order to protect those who gave evidence.