In court papers, they said Morgenthau should be disqualified as a special master in the federal suit because his "distaste" for the mayor means he can't be fair.
"A reasonable person, knowing all the facts, would conclude that Mr. Morgenthau's impartiality could reasonably be questioned," top city lawyer Georgia Pestana wrote.
She also argued that Morgenthau, who was Manhattan district attorney for 35 years before retiring in January, doesn't have enough experience with civil cases.
A federal judge tapped the 90-year-old living legend this week to cut through red tape stalling a new process for hiring firefighters.
Bloomberg clearly isn't ready to submit to this master.
"What is indisputable is Mr. Morgenthau's known distaste for the current city administration - including, in particular, the mayor, the Fire Department and the corporation counsel," Pestanawrote.
The city's motion noted that Morgenthau has locked horns with the administration several times. He tangled with Bloomberg over financial bookkeeping at the District Attorney's office and a grand jury probe into possible negligence by FDNY officials in the deadly Deutsche Bank fire.
Federal Judge Nicholas Garaufis hasn't ruled on the motion, but Morgenthau took the high road.
"My record and independence in my role as district attorney are no secret and I wouldn't have accepted the position if I didn't think I could be impartial," he said in a statement.
"Nonetheless, of course I will do what is in the best interest of moving this important matter forward."
Garaufis ruled last year that two written exams for the Fire Department discriminated against hundreds of black and Hispanic candidates for decades.
Since then, the judge has vented his frustration that the city is "dragging its feet" in carrying out his remedies.
He selected Morgenthau as special master - over candidates offered by the city and prosecutors - to get the process moving.
The city plans to file a more detailed motion next week with more evidence of Morgenthau's supposed bias, including remarks about Bloomberg to Corporation Counsel Michael Cardozo, Pestana said.