By Joseph Ax

NEW YORK (Reuters) - A prominent Manhattan federal judge who has frequently butted heads with U.S. authorities over their handling of financial cases has resigned in protest from a commission that advises the Justice Department on how to use forensic evidence at trial.

In his resignation letter to the National Commission on Forensic Science, U.S. District Judge Jed Rakoff said he felt he "had no choice." He cited the Justice Department's decision that the commission could not consider a proposal he backed to require prosecutors to give more information about forensic experts to criminal defendants before trial.

"Because I believe that this unilateral decision is a major mistake that is likely to significantly erode the effectiveness of the commission - and because I believe it reflects a determination by the Department of Justice to place strategic advantage over a search for the truth - I have decided to resign," Rakoff wrote.

Emily Pierce, a Justice Department spokesman, said in an email the department was "disappointed" in Rakoff's decision.

Rakoff, nominated to the bench by U.S. President Bill Clinton, has been a frequent thorn in the side of the Justice Department and the U.S. Securities and Exchange Commission, criticizing their efforts in pursuing Wall Street for financial crisis-era wrongdoing.

The forensic commission was created in 2013 to help establish national standards, in response to persistent concerns from critics about the quality of evidence used to convict defendants across the country.

In October, the commission's subcommittee on reporting and testimony, co-chaired by Rakoff, recommended to the full commission that prosecutors go beyond current federal criminal rules to provide additional details about scientific expert witnesses' methodology and data to defendants.

The proposal, according to Rakoff, would impose on prosecutors essentially the same requirements that now exist in civil cases.

But the commission was not allowed to consider the merits of the report, after Deputy U.S. Attorney General Sally Yates determined its duties did not include making recommendations about changes to discovery, the process by which adversaries exchange evidence before trial, Rakoff said.

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The decision, he wrote in the letter, appeared to be "designed to preserve a courtroom advantage by avoiding even the possibility that commission discussion might expose it as unfair."

Pierce, the Justice Department spokeswoman, said, "This was a basic disagreement about the scope of the commission's work and many of the proposed recommendations on pretrial discovery are already included in existing rules and Justice Department guidelines."

(Reporting by Joseph Ax; Editing by Noeleen Walder and Richard Chang)