It was a court where the lawyers weren’t really lawyers and justice was a joke, according to one independent study of the New York City Police Department’s internal legal system. The advocates, often members of the rank and file unwillingly roped in to prosecute their peers, rarely issued subpoenas or called witnesses, and the trials regularly took longer than a year to resolve.

Now, thanks to the current NYPD advocate, Julie Schwartz, all of that has changed, police officials say — though not everyone agrees.

“There’s just this assumption that the police department was just a kangaroo court. I think that’s what people were thinking,” Ms. Schwartz said as she ticked off the changes she has implemented since she was hired to run the NYPD Advocate’s Office in 2005. These days, 25 attorneys with law degrees, not reluctant members of the force, examine cases of alleged police misconduct with an experienced legal eye. Many of them are former prosecutors, and some have worked as criminal defense attorneys for Legal Aid. The cases then go to Ms. Schwartz, who was an assistant district attorney in Brooklyn for 15 years, for further scrutiny.

“What I’ve instituted is to try to do more professional cases, to be more professional in the courtroom, to do better legal analysis, to do upfront legal analysis,” she said.

Her reforms have won her frequent praise from the top rungs of the department. But this summer she found herself at the center of a storm of criticism from police watchdog groups.

Among them is the Civilian Complaint Review Board, which investigates complaints of police wrongdoing. Ms. Schwartz rejects the board’s recommendations more frequently than her predecessors did, according to the CCRB and the New York City Civil Liberties Union.

“She’s suggesting that my board is sending over cases that are frivolous, and that they’re sending over cases where they didn’t find a preponderance of evidence. She is second-guessing the board,” the chairwoman of the CCRB board, Franklin Stone, said.

Ms. Stone, who is also a former prosecutor, notes that her board is also mostly made up of lawyers — as it has been for years — who oversee each case before it is forwarded to Ms. Schwartz’s office for review.

The CCRB’s complaints come as the number of citizen reports of police misconduct has risen to the highest level ever, but the use of the harshest punishments against police officers accused of mistreating civilians has plummeted. Instead, Ms. Schwartz’s office more frequently recommends the use of “instructions,” or a talk with the officer’s commander. The CCRB likens such penalties to a slap on the wrist.

The civilian board also noted that Ms. Schwartz’s office is winning convictions in a smaller percentage of cases, though it is conducting fewer trials. Last year, CCRB statistics show that the NYPD Advocate’s Office won nine guilty findings out of 44 cases tried, a 20% success rate, down from around 30% in years past, when twice as many cases were tried.

Ms. Schwartz defends her performance, claiming that since she took charge, fewer cases of the worst misconduct have been substantiated by the complaint agency. The cases coming across her desk these days are more often complaints about “stop, question, and frisk” incidents, she said, in which police officers are accused of the more nebulous crimes of “abusing authority” and being overly aggressive.

It is the increase in accusations involving these gray areas, she suggests, that have made it more difficult to win cases. Ms. Schwartz also argues that “instructions,” rather than harsher punishments, are effective at changing officers’ behavior. She said no officer who has been issued instructions on her watch has come back as a repeat offender for the same type of misconduct.

“The officers have to know that if they do misconduct, they’ll be punished,” she said. “But the stuff that’s coming in is not misconduct.”

As a former assistant district attorney, Ms. Schwartz said she is used to a tense and stressful work environment. Before coming to the police department, she led the Brooklyn district attorney’s sex crimes bureau, where she prosecuted several high profile rape cases. Worn down by the grind of dealing with disturbing sex crimes on a daily basis, she said she applied for the NYPD job for a change of venue. The job is different, if not easier, she said.

“You make a mistake and a rapist gets out,” she said of her old job. “But I never felt so antagonized as in this job.”

Still, she said, she likes the job, and despite their strained relationship, she praises the CCRB for its role in reducing the number of officers who break the rules.

“We’re both trying to keep the city safe, and put the criminals away,” she said. “We have members out there and they need to know that if they make serious misconduct, that they’ll have to face the piper. If we don’t do a good job, and we’re not fair, the message won’t get out there.”