Ex-Home Office chief Sir Philip Rutnam has lodged an employment tribunal claim for unfair dismissal and whistleblowing against Home Secretary Priti Patel.
A statement from the civil servants union the FDA said Sir Philip formally began legal action on Monday.
Sir Philip resigned in February amid bullying claims against Mrs Patel, which she denies.
A government spokesperson said: "We do not comment on ongoing legal proceedings."
Mrs Patel has not commented publicly on the allegations against her, but government sources have said she denies them.
At the time of his resignation, Sir Philip, who was the Home Office's most senior official, said there had been a "vicious and orchestrated" campaign against him.
Announcing the legal action, FDA general secretary Dave Penman said in a statement: "Following his (Sir Philip's) resignation, the FDA instructed Gavin Mansfield QC, head of Littleton Chambers and employment law specialist, as counsel to advise Sir Philip, supported by Clive Howard, senior principal lawyer, employment and partnership at Slater and Gordon.
"This morning, Sir Philip, with the support of his legal team and the FDA, submitted a claim to the employment tribunal for unfair (constructive) dismissal and whistleblowing against the home secretary.
"Sir Philip will not be making any further comment at this time."
A Cabinet Office investigation was launched in March over whether Mrs Patel had breached the ministerial code, amid the bullying allegations.
The prime minister also gave Mrs Patel his support.
In an email to Home Office staff last month, Mrs Patel said she regretted Sir Philip's resignation.
She thanked him for his service but said it was "now time for the Home Office to come together as one team".
She said she "deeply cared" about the "wellbeing" of her civil servants and valued their professionalism.