U.S. District Judge Jed Rakoff, shown here in Sept. 2013, resigned from a commission in protest because he says the Justice Department has muzzled its work. (Yana Paskova/For The Washington Post)

The sole federal judge on a commission appointed by President Obama to improve forensic science in the criminal justice system has resigned in protest, criticizing the U.S. Department of Justice for muzzling its work to benefit prosecutors.

U.S. District Judge Jed S. Rakoff of New York said he quit because the Justice Department had barred it from recommending an expansion of the exchange of pretrial information to include more evidence from forensic experts. Prosecutors routinely share evidence with defense lawyers. Rakoff said in his resignation letter that the ban contradicts the panel’s charter and voids months of work.

The proposed change would address a major criticism of the nation’s top scientific organization and many legal experts, who have warned in recent years that police and prosecutors exercise too much control over crime labs, which suffer from weak standards over research, testimony and examinations. The failings that have led to dozens of lab scandals and hundreds of exonerations over the past two decades.

“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 from the Commission, effective immediately,” Rakoff wrote in an e-mail late Wednesday to fellow commissioners that spread rapidly in legal circles overnight.

“It is hard to escape the conclusion [that the decision] . . . is chiefly designed to preserve a courtroom advantage by avoiding even the possibility that Commission discussion might expose it as unfair,” Rakoff added.

Rakoff’s e-mail came on the eve of the commission’s Thursday meeting, where the evidence discovery proposal was to be discussed. Rakoff wrote that the decision was made by Sally Q. Yates, the department’s acting deputy attorney general since James Cole’s departure Jan. 8, after objections by a vice chairman on the commission, Nelson Santos, head of the U.S. Drug Enforcement Administration’s Office of Forensic Sciences.

Santos did not respond to a request for comment.

In a statement, Justice Department spokeswoman Emily Pierce said, “While the department is disappointed in Judge Rakoff’s decision, this was a basic disagreement about the scope of the commission’s work.”

A department official said its experts found that many of the commission’s proposals were covered by existing rules and guidelines, and encouraged the panel to keep working on evidence retention policies and transparency.

Nevertheless, Rakoff’s departure poses a blow to the credibility of the Obama administration’s effort, announced nearly two years ago, to commit scientists and a new presidentially appointed panel to address recurring concerns about the quality of forensic evidence used in criminal courts across the country.

Rakoff, a 1995 Clinton judicial nominee, made headlines in 2010 and 2011 when he criticized as too lenient the U.S. Securities and Exchange Commission’s treatment of banks involved in the financial crises. He has also been an influential voice from the bench for science, helping revise the 2011 edition of the federal judiciary’s reference manual on scientific evidence and serving on the board of the MacArthur Foundation’s Law & Neuroscience Project.

After meeting for more than a year, the forensic commission has prepared draft recommendations for Attorney General Eric H. Holder Jr. or his nominated successor, Loretta Lynch, to improve evidence discovery and expert testimony, training and certification practices. The commission also reorganized the scientific governing organizations for individual forensic techniques.

The commission’s efforts to improve research, training and standards will likely take years and new resources to bear fruit, however, while participants said Rakoff’s subcommittee on reporting and testimony could immediately help judges and juries make clearer sense of questioned forensic techniques.

Rakoff noted that the commission’s charter explicitly calls for it to develop proposals concerning “the intersection of forensic science and the courtroom.”

“The notion that pre-trial discovery of information pertaining to forensic expert witnesses is beyond the scope of the Commission seems to me clearly contrary to both the letter and the spirit of the Commission’s Charter,” he wrote in his resignation e-mail.

Matthew F. Redle, chief prosecutor for Sheridan County, Wyoming, and co-chair of Rakoff’s subcommittee, said the proposal appeared to have majority support, but Rakoff held it for more discussion to build greater consensus.

“I respect and admire Judge Rakoff a great deal. His letter can speak for itself,” Redle said.

Another commission member, Case Western University law professor Paul C. Giannelli, said he originally disagreed with a 2009 National Academy of Sciences committee report that called for a forensic science agency independent of the Justice Department.

Now, however, he said,“This last development has put the integrity of the whole process into question.”