Since taking office in January 2016, Ms. Clark has tried to walk a tricky line, embracing the correction officers’ complaints, while also stepping up prosecutions of officers accused of misconduct. In the last two years, she has secured indictments against 14 officers on charges ranging from assault to smuggling. Five of the officers have been convicted and the others are awaiting trial.

Her efforts have played out as the city continues its push to improve conditions at the jail complex, which is being overseen by a federal monitor as part of a legal settlement. As part of those reforms, the de Blasio administration has limited solitary confinement, which correction officers saw as a vital tool for maintaining discipline.

In addition to stationing a team of prosecutors on Rikers, Ms. Clark has begun demanding consecutive sentences for inmates who commit crimes on Rikers, greatly increasing the penalties for jailhouse violence.

Some experts on the jail system, however, worry Ms. Clark’s aggressive approach may have unintended consequences. It may load inmates down with additional prison time for jailhouse fights that were in reality acts of self-defense. It also could keep inmates housed in the troubled jail for far longer than necessary, awaiting trial on the new charges.

“I have not seen that this has had any positive effect in terms of controlling violence, and I am concerned that it may actually be keeping people on Rikers Island for extended periods of time who would otherwise be going upstate probably to serve very significant long sentences,” said Dr. Robert L. Cohen, a member of the Board of Correction, which regulates and inspects city correctional facilities.

In her effort to bolster investigations of guards, Ms. Clark formed a public integrity bureau and made it responsible for examining allegations of misconduct by correction officers.