This spring, however, a federal judge in Brooklyn issued a potentially influential order in a wrongful-conviction case in Queens, saying that under a 2009 Supreme Court ruling, issues related to the “supervision and training” of assistant district attorneys were not administrative matters, but prosecutorial ones, and so the city could not be held accountable for them.

Image Judge Ann Marie Donnelly of the Federal District Court in Brooklyn.

Last week, a coalition of defense lawyers filed an appellate brief attacking the order and claiming that it could stop people wronged by prosecutors from seeking any form of financial redress. Moreover, the lawyer said, it could also cripple efforts to hold prosecutors responsible for ethical or legal violations.

The ruling by the judge, Ann M. Donnelly, a former prosecutor, “threatens to eliminate (or, at the very least, substantially limit) municipal liability for prosecutorial misconduct,” according to the brief, which was filed by the Innocence Project and the National and New York State Associations of Criminal Defense Lawyers. If neither the state nor individual prosecutors can be sued, the brief said, then Judge Donnelly’s ruling barring most suits against the city could mean that there would be no way for defendants to be compensated for — or to force changes in — a “D.A.’s unconstitutional or deliberately indifferent policy decisions.”

Both the ruling and the brief came in the case of Kareem Bellamy, who was found guilty in 1995 of stabbing a man to death outside a C-Town supermarket in Rockaway, Queens. After he spent 13 years in prison, Mr. Bellamy’s conviction was overturned by a State Supreme Court judge who determined that someone else had committed the murder. Though the Queens district attorney’s office initially contested the reversal, it dismissed the indictment against Mr. Bellamy in September 2011. Six months later, he filed suit against two police officers who worked on his case, and also sued the district attorney’s office, accusing it of having an illegal policy in place that helped convict him.

According to depositions in the lawsuit, that policy established a so-called “Chinese wall” closing off communication between prosecutors in the Queens witness protection program who provided security for people testifying at criminal proceedings and the rank-and-file prosecutors who tried defendants like Mr. Bellamy in court. The lawsuit claims that the wall was designed to keep trial prosecutors unaware of any deals with witnesses that encouraged them to testify. That way, it maintains, the trial prosecutors could accurately tell a jury that they had no personal knowledge of agreements reached with witnesses.