Boris Johnson has seen off a High Court challenge over his decision to back Home Secretary Priti Patel following accusations she bullied civil servants.
The FDA, which represents civil servants, brought the judicial review after the Prime Minister overruled a report into Ms Patel's behaviour by his independent standards advisor Sir Alex Allan last year.
Sir Alex said Ms Patel's conduct "amounted to behaviour that can be described as bullying" in a damning report last November.
He said this included "shouting and swearing" at her staff and ruled that she had not always treated civil servants with "consideration and respect".
Sir Alex concluded that Ms Patel had broken the ministerial code, even if it was done "unintentionally", for which a minister would normally be expected to resign.
But the Prime Minister, who is the arbiter of the ministerial code, decided to disregard Sir Alex's advice.
Mr Johnson said the Home Secretary was "unaware" of the impact she had and he was "reassured" she was "sorry for inadvertently upsetting those with whom she was working".
After "weighing up all the factors", he concluded the code had not been breached.
At the time, Ms Patel issued an "unreserved, fulsome apology" and said there were "no excuses" for what happened.
Sir Alex later resigned from his post.
At a hearing last month, lawyers for the FDA argued that the PM had "misinterpreted" the term "bullying" in the Ministerial Code when deciding if Ms Patel's treatment of civil servants breached its standards.
They alleged he made a "misdirection of law" in reaching his decision.
Lawyers for Mr Johnson argued that the FDA's claim was "not justiciable" and that there had been "no error of law".
They said the Ministerial Code "does not create or impose any legal duties on ministers or the Prime Minister", is "not required by law", and its contents are "not regulated by law".
The code is a "political document" and "not about protecting the rights of civil servants" who still have access "to all the employment law rights", the Prime Minister's lawyer argued.
Lord Justice Lewis concluded in a ruling at the High Court on Monday that Boris Johnson had not misdirected himself.
The judge, sitting with Mrs Justice Steyn, said: "The question for this court is whether the Prime Minister proceeded on the basis that conduct would not fall within the description of bullying within paragraph 1.2 of the Ministerial Code if the person concerned was unaware of, or did not intend, the harm or offence caused.
"Reading the statement (made by Mr Johnson) as a whole, and in context, we do not consider that the Prime Minister misdirected himself in that way."
FDA general secretary Dave Penman said despite the overall dismissal of the union's claim, the judgment was an "important step forward in the battle to ensure that ministers are held to account for their behaviour in the workplace".
He said: "The court has determined that the Prime Minister did not acquit the Home Secretary of bullying, and that he did not reject the findings of Sir Alex Allan that her conduct amounted to bullying.
"This will bring some comfort to those civil servants who were brave enough to come forward and give evidence to the investigation about the Home Secretary's conduct.
"While the court decided that the Prime Minister was entitled not to dismiss the Home Secretary, the case has important implications for the protection of civil servants in the future."
The union said it will apply for its legal costs to be paid in full by the Government given the findings made in the ruling, despite the overall dismissal.
