Boris Johnson drove his own ethics adviser to quit on Friday as he ripped up the rulebook by refusing to sack Priti Patel despite a formal investigation finding evidence that she bullied civil servants. After a Cabinet Office inquiry, Sir Alex Allan said the home secretary’s conduct “amounted to behaviour that can be described as bullying” – noting instances of shouting and swearing, and finding that she had breached the ministerial code, even if unintentionally. Johnson seized on that caveat, seemingly dismissing the report, by insisting he judged the code had not been breached – and he had full confidence in Patel. He then urged Tory colleagues in a WhatsApp message to “form a square around the Prittster”. In a statement issued at the same time as the prime minister’s decision, Allan, who also served Johnson’s two predecessors, said: “I feel that it is right that I should now resign from my position as the prime minister’s independent adviser on the code.” Late on Friday night, Downing Street failed to deny reports that the prime minister had tried to persuade Allan to tone down his conclusions to find there was no clear evidence of bullying. A No 10 spokesman 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.” The 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. Dave Penman, the general secretary of the FDA union for senior civil servants, said Johnson’s decision to ignore the report’s findings meant “no civil servant will now have confidence that any complaint raised about ministerial behaviour will be dealt with fairly or impartially”. Jonathan Evans, the chair of the committee on standards in public life, called Allan’s resignation “deeply concerning” and added: “This episode raises serious questions about the effectiveness of the current arrangements for investigating and responding to breaches of the ministerial code.” Patel later apologised, saying in a broadcast interview on Friday evening: “I’m sorry that my behaviour has upset people and I have never intentionally set out to upset anyone. I work with thousands of brilliant civil servants every single day and we work together, day in day out, to deliver on the agenda of this government and I’m absolutely sorry for anyone that I have upset.” However, Sir Philip Rutnam, who resigned as the Home Office’s permanent secretary after accusing Patel of a “vicious and orchestrated briefing campaign” against him, added to the pressure on Patel by challenging a claim in the bullying report that she had been given no feedback about her behaviour by civil servants, and was therefore unaware of the impact. “This is not correct,” Rutnam said. “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.” In another remarkable admission, he said he was “at no stage asked to contribute evidence to the Cabinet Office investigation”. Johnson’s decision to stand by Patel provoked fury among opposition MPs. The Labour leader, Sir Keir Starmer, said: “If I were prime minister, the home secretary would have been removed from her job. “It is hard to imagine another workplace in the UK where this behaviour would be condoned by those at the top.” No 10’s determination to brazen out the row has echoes of the prime minister’s handling of Dominic Cummings’ lockdown trip to Barnard Castle. A statement from Downing Street insisted: “The prime minister has full confidence in the home secretary and considers this matter now closed.” Conservative MPs largely rallied behind Patel, the MP for Witham, who was a leading figure in the Vote Leave campaign alongside Johnson and the Cabinet Office minister Michael Gove. Johnson’s new press secretary, Allegra Stratton, said of the prime minister: “He loathes bullying. He takes it very seriously and recognises that it is very difficult for people to come forward and raise concerns. It’s a brave thing to do, he knows that, and he believes that this process has been thorough. But it is also his responsibility to look at … the conclusions in the round.” Asked about the “Prittster” message, she said it reflected an acknowledgment that “this is a testing day for her”. The decision came on day five of Johnson’s “reset”, after a tumultuous period in No 10 last week that ended with the resignations of his two key aides, Cummings and Lee Cain. But the outcome of the Patel inquiry, which has been sitting on Johnson’s desk for weeks, is unlikely to reassure civil servants, who may have hoped for a letup in the “hard rain” Cummings had promised would fall on Whitehall. Johnson did not appear in public himself on Friday, with the health and social care secretary, Matt Hancock, fronting a Downing Street press conference. Asked what the point was of having an independent adviser on ministerial standards if the prime minister ignored the advice when it was “one of his mates in the firing line”, Hancock said: “The prime minister has been clear that he doesn’t think that the home secretary has broken the ministerial code.” Rutnam has lodged an employment tribunal claim against Patel under whistleblowing laws, claiming he faced constructive dismissal after informing the Cabinet Office of the home secretary’s behaviour. Downing Street only published a one-and-a-half page summary of Allan’s report, which included criticism of the culture in the Home Office, a notoriously dysfunctional department. Patel’s predecessor, Amber Rudd, resigned over the Windrush scandal. “The civil service itself needs to reflect on its role during this period,” Allan’s report said. “The Home Office was not as flexible as it could have been in responding to the home secretary’s requests and direction. She has – legitimately – not always felt supported by the department.” In its statement, Downing Street said: “The prime minister notes Sir Alex’s advice that many of the concerns now raised were not raised at the time and that the home secretary was unaware of the impact that she had. He is reassured that the home secretary is sorry for inadvertently upsetting those with whom she was working.” It added: “As the arbiter of the code, having considered Sir Alex’s advice and weighing up all the factors, the prime minister’s judgment is that the ministerial code was not breached.” The chair of the home affairs select committee, Yvette Cooper, who repeatedly pressed Rudd over Windrush, called on the government to publish Allan’s report in full. “The issues raised by Sir Alex Allan’s inquiry are extremely serious, and his resignation in the light of the prime minister’s response makes them doubly so. I am therefore asking the cabinet secretary to provide the home affairs select committee with a copy of the full report as a first step so that we can consider the issues it raises on misconduct, bullying and the operations of the Home Office,” she said. “Public servants working in government departments must never be bullied by ministers or treated with disrespect, and they need to know there are standards and safeguards in place to prevent that happening.”