A legal challenge has been launched against Boris Johnson’s decision to clear Priti Patel of bullying despite advice that she had breached the ministerial code.

Lawyers for the FDA union sent a pre-action notice to Downing Street on Wednesday accusing the prime minister of acting unlawfully when he chose to stand by his home secretary and overrule his independent adviser.

The letter, first reported in the Times, accuses Johnson of “setting a damaging precedent which gives carte blanche to the kind of unacceptable conduct which the home secretary was found to have committed”.

The union hopes the letter is the first step towards a judicial review of Johnson’s decision. The government has so far refused to make public the full Cabinet Office investigation led by Sir Alex Allan, which concluded that Patel’s actions amounted to bullying.

The government is expected to fight any legal challenge against Johnson’s decision.

The move comes after Jonathan Evans, the chair of the committee for standards in public life, launched a review of probity rules, which will include the ministerial code.

Dave Penman, the general secretary of the FDA, told the Guardian: “The prime minister’s decision has laid bare the inadequacies of the ministerial code as a mechanism for dealing with the conduct of ministers when it comes to their civil servants. The code provides no commitments or rights to the civil servants who were bullied by the home secretary nor any mechanism for challenge.

“Unless this perverse decision by the prime minister, ignoring the evidence provided to him, can be challenged in the courts, it essentially deprives civil servants of the very protection against ministerial misconduct which the code is meant to ensure.”

Allan resigned last month after Johnson reportedly tried to persuade him to tone down the report.

Overruling his adviser on ministerial standards, Johnson acknowledged that while Allan had concluded Patel’s behaviour could “on occasion” be described “as bullying in terms of the impact felt by individuals”, he had “full confidence” in the cabinet minister.

The legal letter sent on Wednesday states: “Civil servants in the Home Office and beyond will rightly object to their conduct being measured against a standard of conduct and unacceptable bullying which, it seems, does not apply to the home secretary or other ministers.”

Sir Philip Rutnam, who quit as the department’s permanent secretary after accusing Patel of a “vicious and orchestrated briefing campaign” against him, is taking the home secretary to an employment tribunal in September.

He claims he was forced out following anonymous briefings after blowing the whistle on her behaviour. Patel denies all allegations against her.

The government has been approached for a comment.