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Boris Johnson has judged that his Home Secretary had not breached the ministerial code despite Sir Alex concluding that she had “not consistently met the high standards expected of her”.
A Government statement said Mr Johnson has “full confidence” in Ms Patel and “considers this matter now closed”.
Ms Patel has apologised for upset caused by her behaviour, saying in a statement: “It has never been my intention to cause upset to anyone.”
Normally ministers are expected to resign if they breach the code.
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 the Home Office’s permanent secretary Sir Philip Rutnam, who accused Ms Patel of a “vicious and orchestrated briefing campaign” against him and is claiming constructive dismissal at an employment tribunal.
Announcing his resignation on Friday, Sir Alex said in a statement: “I recognise that it is for the Prime Minister to make a judgment 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.”
Sir Alex said Ms Patel’s frustrations had seen her shout and swear in some instances.
In his published advice, he said: “She is action-orientated and can be direct.
“The Home Secretary has also 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 now defunct Department for International Development) three years ago.
“The evidence is that this has manifested itself in forceful expression, including some occasions of shouting and swearing.
“This may not be done intentionally to cause upset, but that has been the effect on some individuals.”
Responding to the report’s findings, Ms Patel admitted her “directness” and said she had “at times got frustated” while delivering on Government commitments.
She said in a statement: “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.”
Matthew Rycroft, permanent secretary in the department, said relationships between officials and ministers had “improved considerably” but admitted the report into the Home Secretary’s conduct made for “difficult reading”.
He 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.”
Labour leader Sir Keir Starmer has condemned Mr Johnson’s decision to keep Ms Patel in her post.
“Yet again, the Prime Minister has been found wanting when his leadership has been tested. If I were Prime Minister, the Home Secretary would have been removed from her job,” he said in a statement.
“It is hard to imagine another workplace in the UK where this behaviour would be condoned by those at the top.
“The Government should be setting an example. Instead, it is one rule for Boris Johnson and his friends, another for everyone else.
“The Prime Minister has previously said he ‘loathes bullying’. Yet when one of his own ministers is found to have bullied their staff he ignores the damning report sat on his desk and instead protects them.
“In the interest of transparency, the report into Priti Patel’s conduct and any drafts should now be fully published and the Prime Minister and Home Secretary should come to the House on Monday to face questions on their conduct.”
Yet again, the Prime Minister has been found wanting when his leadership has been tested.
If I were Prime Minister, the Home Secretary would have been removed from her job. [Thread]
— Keir Starmer (@Keir_Starmer) November 20, 2020
Labour is demanding the publication of the full inquiry findings, with Shadow home secretary Nick Thomas-Symonds accusing the PM of being “engaged in a cover-up”.
Calling for the immediate publication of the full Cabinet Office findings, he said: “These revelations could not be more serious.
“This has all the hallmarks of a cover-up from the Prime Minister and raises fundamental questions about his judgment.
“His actions are all but condoning bullying in the workplace. In any other area of life this would not be acceptable. Yet again, it seems to be one rule for them and another for everyone else.
“The report needs to be published in full immediately and both the Prime Minister and Home Secretary must come before Parliament to answer questions on this mess.”
Mr Thomas-Symonds said he had written to the chairman of the Committee on Standards in Public Life – former MI5 director general Lord Evans of Weardale – asking him to investigate Ms Patel’s conduct.
Dave Penman, general secretary of senior civil servants’ union the FDA, said Mr Johnson’s actions had undermined confidence in the whole process.
“In his foreword to the ministerial code, Boris Johnson said: ‘There must be no bullying and no harassment,’” he said.
“If, as is being suggested, substance has been found in some of the allegations against the Home Secretary, then the Prime Minister should have no choice but to conclude that the code has been breached.
“As Prime Minister, he is the sole arbiter of the ministerial code but he is also Minister for the Civil Service.
“Having pledged his support for the Home Secretary when the investigation began, and now sat on the report since the summer, he has already undermined confidence in this being a fair and impartial process.”