A federal judge in New York on Monday ruled against President Donald Trump and the Justice Department over the firing of Maurene Comey, daughter of former FBI Director James Comey, from the Manhattan U.S. attorney's office. Judge Jesse Furman said Comey's termination violated civil service rules. "Yes, the Attorney General is authorized by law to remove an AUSA.

But the Attorney General (and anyone to whom the Attorney General delegates that authority) is also limited by law, namely the CSRA, to do so only in a particular manner and only for certain reasons," the judge wrote.

Furman ordered Maurene Comey, who most recently led the prosecution of Sean "Diddy" Combs, reinstated with back pay.

In addition to calling her termination unlawful, Furman decided Trump and the DOJ violated the separation of powers, the Administrative Procedure Act and Maurene Comey's due process rights.

"The Department disagrees with this decision and will appeal in due course," a DOJ spokesperson told ABC News. A spokesperson for the U.S. Attorney's Office for the Southern District of New York declined to comment. ABC News has reached out to Maurene Comey for comment.

Furman's ruling outlines that Maurene Comey's reinstatement applies from the date of her termination in July of 2025 until December, when she effectively resigned from her role by accepting a new job in the private sector.

In ordering Maurene Comey's reinstatement, Furman rejected what he described as the Trump administration's "sweeping and unprecedented theory of executive authority." The Trump administration had argued that not only was Maurene Comey's firing lawful under federal statute, but that the laws protecting civil servants were also an unconstitutional intrusion into Trump's authority.

"The question at the heart of this case is whether these limitations on the removal of Assistant United States Attorneys are consistent with Article II and the constitutional separation of powers," Judge Furman wrote.

To make its argument, the DOJ pointed to the Supreme Court's decision in Trump v. Slaughter -- where the justices effectively supercharged presidential power by greenlighting the firing of the leaders of independent federal agencies -- and the Trump v. United States immunity case "On their view, AUSAs who represent the United States in criminal cases in court exercise prosecutorial and investigatory functions that fall squarely within the President's 'conclusive and preclusive' powers," Furman wrote. "Accordingly, they argue, the President -- and, by extension, the heads of departments appointed by the President -- must have the power to remove such AUSAs for any reason or no reason at all."

But Furman rejected the DOJ's interpretation of the legal precedent, pointing to decades of other cases which affirm the legal protections for line prosecutors. He also noted that neither case cited by the DOJ applies to inferior officers or "supports their sweeping and unprecedented theory of executive authority." "Defendants' argument is contrary to an unbroken line of Supreme Court decisions dating back almost two centuries, and the Supreme Court itself has not formally overruled any of those decisions. That is sufficient, in itself, to reject the argument," wrote Judge Furman.

To accept the DOJ's argument, Furman wrote, would "unsettle the very equilibrium established by this Nation's constitutional system." Maurene Comey was an assistant U.S. attorney who successfully prosecuted Ghislaine Maxwell, the former associate of sex offender Jeffrey Epstein, and multiple gang members before the split verdict last year in the trial of Combs, who was convicted of a prostitution-related charge but acquitted of more serious charges.

She was also involved in the office's case against Epstein, who died by suicide in 2019 at New York City's Metropolitan Correctional Center while he was awaiting trial on federal sex trafficking charges.

Trump fired James Comey during his first term in office after Comey announced publicly that Trump's 2016 campaign was being investigated over potential ties to Russia.

Prior to Maurene Comey's firing, Trump privately vented about having a Comey work in his administration, sources previously told ABC News.

Earlier this year, Furman blocked the Justice Department's attempt to move Maurene Comey's lawsuit over her firing as a federal prosecutor out of court.

The Justice Department argued at the time that her case belongs before the Merit Systems Protection Board and not in federal district court.

Furman decided the case belongs with him because Maurene Comey was fired pursuant to the president's executive authority and not the usual procedures for civil servants.

"Maurene Comey was, by all accounts, an exemplary Assistant United States Attorney. In her nearly ten years working at the United States Attorney's Office for the Southern District of New York, she was assigned some of the country's highest profile cases, and she consistently received the highest accolades from supervisors and peers alike," the judge's opinion in April said. The DOJ, in court filings, has characterized Comey's case as routine.

"A federal employee's claims that removal from federal service was arbitrary and capricious or conducted in a manner that did not provide the process to which they contend they were due is not a novel issue," government attorneys previously said.

Following her termination last year, Maurene Comey told colleagues in a farewell email that she was fired as a federal prosecutor without being told a reason but urged them not to succumb to the "fear" she said her firing could cause.

"If a career prosecutor can be fired without reason, fear may seep into the decision of those who remain," Comey said in her email, a copy of which was obtained by ABC News. "Do not let that happen."