Boris Johnson’s adviser on ministerial standards has resigned after the Prime Minister contradicted his advice by judging that Priti Patel did not breach the rules despite being found to have bullied staff.

Sir Alex Allan said the Home Secretary 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 said there was “no evidence that she was aware of the impact of her behaviour”.

But Mr Johnson, who is arbiter of the code, judged that Ms Patel did not breach the rules. He continues to have “full confidence” in the Home Secretary and “considers this matter now closed”, according to a Government statement.

Sir Alex resigned in response to Mr Johnson’s verdict, saying in a statement: “I recognise that it is for the Prime Minister to make a judgement on whether actions by a Minister amount to a breach of the ministerial code.

“But I feel that it is right that I should now resign from my position as the Prime Minister’s independent adviser on the code.”

Ms Patel issued an “unreserved, fulsome apology” and said there were “no excuses” for what happened.

She told the BBC: “I have clearly upset people in the past and on reflection – and I have had time to reflect upon this as well – looking at what has been published today on the report, there is no question I’m absolutely sorry for the upset that has been caused and I’m very, very clear about that.”

Ms Patel said she wanted to change the “culture and ways of working” in the Home Office, but noted that it was a “challenging department” where “we’re making life and death decisions every single day”.

Ministers are usually expected to resign if they breach the code, and Mr Johnson’s decision to stand by Ms Patel sparked fury from opposition MPs.

Labour leader Sir Keir Starmer said: “It is hard to imagine another workplace in the UK where this behaviour would be condoned by those at the top.”

Jess Phillips, shadow minister for domestic violence, said it was an “utter disgrace” and that any Conservative MP “seeking to defend this is utterly without reason or comprehension”.

Sir Alex concluded that Ms Patel’s behaviour – which was said to include some occasions of shouting and swearing – met the definition of bullying adopted by the civil service.

In his advice published on Friday morning during Anti-Bullying Week, he said: “The definition of bullying adopted by the Civil Service accepts that legitimate, reasonable and constructive criticism of a worker’s performance will not amount to bullying.

“It defines bullying as intimidating or insulting behaviour that makes an individual feel uncomfortable, frightened, less respected or put down. Instances of the behaviour reported to the Cabinet Office would meet such a definition.”

He added: “Her approach on occasions has amounted to behaviour that can be described as bullying in terms of the impact felt by individuals. To that extent her behaviour has been in breach of the ministerial code, even if unintentionally.”

However, he said there was “no evidence that she was aware of the impact of her behaviour, and no feedback was given to her at the time”.

He added: “The high pressure and demands of the role, in the Home Office, coupled with the need for more supportive leadership from the top of the department has clearly been a contributory factor.

“In particular, I note the finding of different and more positive behaviour since these issues were raised with her.”

Matthew Rycroft, permanent secretary at the Home Office, said relationships between officials and ministers at the department had “improved considerably” but admitted the report made for “difficult reading”.

However Sir Philip Rutnam, who resigned as the Home Office’s permanent secretary under Ms Patel, contested Sir Alex’s advice.

He said he had advised the Home Secretary not to “swear and shout” at staff last year, and said he was “at no stage asked to contribute evidence to the Cabinet Office investigation”.

He said: “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.

“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.”

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.

The FDA union, which represents senior public servants, said Mr Johnson had made a “brazen political choice” to keep Ms Patel in office and called for an independent process to be established.

General secretary Dave Penman told the PA news agency: “He has a moral obligation to apply to the standards in the ministerial code fairly and impartially and he has just blatantly ignored that.”

Mr Johnson’s press secretary Allegra Stratton said the Prime Minister “loathes bullying” and takes the allegations “seriously”, but did not consider Ms Patel to be a bully.

Ms Stratton told a Westminster briefing: “These were extremely serious allegations that were made and that have been dealt with in detail, not just by Sir Alex Allan but also by the Prime Minister.

“The Prime Minister does personally take these allegations exceedingly seriously. He loathes bullying. He takes it very seriously and recognises that it is very difficult for people to come forward and raise concerns. It is a brave thing to do. He knows that.

“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.

A Cabinet Office investigation was launched in March over allegations that Ms Patel belittled colleagues and clashed with senior officials in three different departments.

It followed the resignation of then-permanent secretary Sir Philip who accused Ms Patel of a “vicious and orchestrated briefing campaign” against him and is claiming constructive dismissal at an employment tribunal.