Boris Johnson on Friday night urged his MPs to "form a square around the Prittster" as a bitter war of words broke out between the Prime Minister and civil servants.

In a WhatsApp message, Mr Johnson rallied MPs to back Priti Patel after he refused to sack her for an alleged breach of the ministerial code and declared he had "full confidence" in her as Home Secretary.

He rejected the findings of an inquiry by Sir Alex Allan, the Government’s ethics adviser, that Ms Patel had bullied civil servants, albeit unintentionally, and that she had not consistently met the standards required by the ministerial code.

Instead, Mr Johnson pointed to findings in Sir Alex’s report that Ms Patel had been "justifiably frustrated" in many instances by obstructive mandarins’ "lack of responsiveness and support" and failure to give her any feedback on the impact of her behaviour.

His decision to back Ms Patel – who on Friday issued a "fulsome and unreserved apology" to anyone she had upset – prompted the resignation of Sir Alex and a backlash from some of the country’s most senior former mandarins.

Boris Johnson's decision to back Ms Patel prompted a backlash

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Lord Evans, the chairman of the committee on standards in public life, which advises the Prime Minister on ethics, said it was "deeply concerning" that Sir Alex, "a man of great wisdom and integrity", had resigned.

The former MI5 chief said he would be "urgently" looking into the "effectiveness of the current arrangements for investigating and responding to breaches of the ministerial code" as part of a wider review of ethics in public life. He added that the case highlighted his concern over the "lack of independence" in the way breaches were investigated, which meant Mr Johnson was caught between "his political judgment" and "standards issues".

The former Cabinet Secretary Lord O’Donnell said Ms Patel should have resigned, adding: "The Prime Minister thinks there has been no breach of the ministerial code. I, personally, take the judgment of Alex Allan that actually there was a breach of the ministerial code."

Lord Kerslake, a former head of the Civil Service, said Ms Patel’s failure to quit was "reprehensible". "It is absolutely a clear-cut breach of the code on a very serious issue of bullying. In those circumstances in any other time the minister would have gone," he said.

Sir Philip Rutnam, whose resignation as the Home Office’s top mandarin and claims of bullying by Ms Patel prompted the inquiry, issued a statement disputing Sir Alex’s findings, claiming the Home Secretary had been advised not to "shout and swear at staff" a month after her appointment in July last year.

"I advised her on a number of further occasions between September 2019 and February 2020 about the need to treat staff with respect," he claimed, also denying that he had been obstructive.

In a statement, however, Mr Johnson said he did not believe Ms Patel had breached the code and considered "the matter now closed".

His press secretary, Allegra Stratton, said: "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."

Repeating her apology in a TV interview on Friday night, Ms Patel said: "I’m here to give an unreserved apology today and I am sorry if I have upset people in any way whatsoever. That was completely unintentional."

A source said: "Sir Alex said she was not supported, the civil service was inflexible and there was no feedback on the impact that her behaviour was having. She asked for things, requested things and they ignored her. That is not what the civil service are there to do."

Another ally added: "I don’t see why she is apologising. It should be the civil service that is apologising."

The former Tory leader Iain Duncan Smith said: "MPs will support her. The WhatsApps groups are full of support for her. The Prime Minister is right to back her."