Boris Johnson's decision not to sack Priti Patel after a report found evidence she bullied officials will be challenged in the courts.
The FDA union, which represents civil servants, said it was launching a judicial review to challenge Mr Johnson's decision to disregard a report in November that found the Home Secretary had breached the ministerial code.
The Prime Minister overruled the advice of his independent adviser on ministerial standards, Sir Alex Allan, who found Ms Patel's conduct "amounted to behaviour that can be described as bullying", including incidents of "shouting and swearing" at staff.
Sir Alex said the Cabinet Minister had breached the code, even if it was done "unintentionally".
Ministers are usually expected to resign if they breach the code but Mr Johnson, who is its arbiter, stood by Ms Patel.
Sir Alex resigned after Mr Johnson rejected his advice.
The FDA union branded the PM's decision "extraordinary" in the face of evidence that Ms Patel had bullied civil servants.
FDA General Secretary Dave Penman said: “As the union that represents many of the staff who work day to day with ministers, we cannot simply let this issue rest.
"Civil servants should expect to work with ministers without fear of being bullied or harassed.
"Warm words from the Prime Minister have no meaning if the process for addressing those behaviours has been fundamentally undermined by his actions.
“His decision, which he said reflected the Home Secretary’s assertion that her actions were unintentional, also potentially allows ministers to avoid the consequences of their behaviour in future by pleading that it should be the intent of their actions which is important, not the consequences.
“Our judicial review, launched today, would seek to overturn the Prime Minister’s decision that the Home Secretary's conduct did not breach the Ministerial Code.
"This is not about whether the Home Secretary should be forced to resign, that is a matter for the Prime Minister, this is simply about how the Ministerial Code is interpreted."
A survey of FDA members who are most likely to work with ministers, nearly 90% said they had no confidence in the Ministerial Code as a mechanism for dealing with bullying and harassment by ministers, he said.
Following the publication of Sir Alex's report, Ms Patel issued an "unreserved, fulsome apology" and said there were "no excuses" for what happened.
