Officers documented 7,283 searches after stops in 2014, according to Police Department data contained in the report. Of those, one in 12 resulted in a complaint to the review board, a frequency that has increased sharply over past two years. In many cases, Mr. Emery said, the problem could be resolved by requiring further training.

“We are sympathetic to the officers who have been forced to do things that the Police Department should have known was wrong,” Mr. Emery said, speaking of the years during the Bloomberg administration when officers engaged in record numbers of stop-and-frisk encounters.

Mr. Emery also said the review agency had worked to speed up its investigations, with some now conducted in less than three months; that reduces the time officers work under the cloud of an unresolved complaint. “It is a bureaucracy that is in a state of turnaround,” he said.

Mr. Emery, who took over as chairman in July, has made a point of trying to align the agency’s recommendations for discipline more closely with what is ultimately imposed by the police commissioner, William J. Bratton, who is a friend.

Image Patrick J. Lynch, the president of the largest police union, has called for complaints from civilians to be taken under oath. Credit... John Minchillo/Associated Press

One new policy in particular, highlighted in the report, has drawn scrutiny: allowing the Police Department to send back discipline recommendations for “reconsideration” of penalties and, in some cases, the agency’s finding of fault. The New York Civil Liberties Union has strongly opposed the new policy since it was proposed last year.

Since October, the Police Department has sent back cases involving 41 officers, roughly 18 percent of the officers in substantiated cases. Of those, the review board decided to lower its recommended penalties for 23 officers, increased it for two officers and exonerated four others after originally substantiating the claim against them.