Boris Johnson’s influential adviser on ministerial interests has quit the government after the prime minister stood by Priti Patel – despite an internal investigation finding her guilty of bullying.

Sir Alex Allan walked out after advising Johnson that Patel’s approach towards Home Office staff, which included “shouting and swearing”, was “behaviour that can be described as bullying” and that the home secretary had therefore “not consistently met the high standards expected of her under the ministerial code”.

Allan also said he was using the civil service definition of bullying as “intimidating or insulting behaviour that makes an individual feel uncomfortable, frightened, less respected or put down”.

But Johnson overruled his adviser and judged that the code “was not breached”, insisting that concerns about Patel were not raised at the time and that she was unaware of the impact of her behaviour.

Ex-MI5 boss Lord Evans, chair of PM’s committee on standards in public life, said Allan’s resignation was “deeply concerning” and “raises serious questions about the effectiveness of the current arrangements for investigating and responding to breaches of the ministerial code”, which he will address as part of an ongoing review.

The home secretary kept her job after saying she was “sorry that my behaviour in the past has upset people”.

Later, Johnson’s press secretary Allegra Stratton said the PM had told staff on Friday that he “will not tolerate bullying” and that “it is not his belief that Patel is a bully”.

Stratton also confirmed that Johnson texted Tory MPs telling them to “form a square around the prittster”.

“He wanted her parliamentary colleagues to support her in acknowledging that this is a testing day for her,” Stratton told reporters.

A government statement said that Allan advised the PM that there were “difficult working relationships all round” between Patel and Home Office staff.

His advice “found that the home secretary had become – justifiably in many instances – frustrated by the Home Office leadership’s lack of responsiveness and the lack of support she felt in DfID [the international development department] three years ago.

“He also found, however, that the home secretary had not always treated her civil servants with the consideration and respect that would be expected, and her approach on occasion has amounted to behaviour that can be described as bullying in terms of the impact felt by individuals.

“He went on to advise, therefore, that the home secretary had not consistently met the high standards expected of her under the ministerial code.” 

The statement went on to say that Johnson “is reassured that the home secretary is sorry for inadvertently upsetting those with whom she was working.

“He is also reassured that relationships, practices and culture in the Home Office are much improved.

“As the arbiter of the code, having considered Sir Alex’s advice and weighing up all the factors, the prime minister’s judgement is that the ministerial code was not breached.”

But delivering his resignation, Allan, who has been a civil servant for decades, said: “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.

“The prime minister has full confidence in the home secretary and considers this matter now closed.”

In a statement, Patel said: “I am sorry that my behaviour in the past has upset people. It has never been my intention to cause upset to anyone.

“I am very grateful for the hard work of thousands of civil servants who help to deliver the government’s agenda.

“I care deeply about delivering on the commitments we have made to the people of this country and I acknowledge that I am direct and have at times got frustrated.

“I would like to thank the prime minister for his support. The permanent secretary and I are working closely together to deliver on the vital job the Home Office has to do for the country.”

Home Office permanent secretary Matthew Rycroft said: “Sir Alex Allan’s findings make difficult reading, including for the civil service.

“The Home Secretary and I are committed to working together to improve the Home Office and build the strongest possible partnership between ministers and officials based on support, candour, safety to challenge, mutual respect and professionalism. Relationships between ministers and officials have improved considerably. 

“Day in day out Home Office staff work tirelessly to keep the public safe, cut crime, and improve our immigration and asylum system, and we are determined that they should do so in a supportive environment that respects their wellbeing.”