And this month, the Bronx district attorney declined to prosecute guards and supervisors involved in a 2012 assault on two inmates who witnesses said were handcuffed to gurneys and beaten until blood splattered the walls around them. The assault was previously reported in The Times, recommended twice for prosecution by the city’s Investigation Department and cited in the United States attorney’s report.

After many of the violent episodes, according to the federal inquiry, guards and their supervisors falsified use of force reports to cover up brutal behavior.

The investigative division under Ms. Finkle was described in the United States attorney’s report as overwhelmed by the number of cases and largely ineffectual. A small staff and paper-based record keeping hinder investigations, which are supposed to take five months but often take over a year, the report said.

Current and former colleagues said Ms. Finkle had desperately tried to improve conditions at Rikers and weed out troublesome guards, but frequently encountered resistance from both uniformed staff and high-level department officials.

Her efforts often ran up against the powerful correction officers’ union, led by Norman Seabrook.

Several times, according to correction officials, Mr. Seabrook personally thwarted attempts by Ms. Finkle to crack down on violence by guards. On more than one occasion he has publicly called for her resignation, describing her efforts to investigate correction officers as a witch hunt. According to two former investigators, Mr. Seabrook once marched into her office unannounced, threatening to get her fired.

In an interview, Mr. Seabrook denied he had confronted her, but made it clear he was glad Ms. Finkle stepped down. Contrary to the United States attorney’s report, he said, she was heavy-handed and overly hard on officers.

“She’d use a hammer to kill a fly,” he said, criticizing her for seeking more severe penalties for officers who were found guilty of using excessive force than administrative judges had imposed.