A New York City correction officer was arrested on Monday by the Federal Bureau of Investigation and charged with violating the civil rights of a mentally ill inmate who died after begging for medical help from his cell for hours.

The officer, Terrence Pendergrass, was supervising the Rikers Island unit where the prisoner was being held and, according to the criminal complaint filed Monday, Mr. Pendergrass ignored subordinates who warned that the prisoner, Jason Echevarria, was in distress and needed aid. Mr. Echevarria, who was 25, was found dead hours later.

The charge in the August 2012 death comes as the city faces mounting scrutiny over conditions on Rikers Island and in particular the treatment of mentally ill inmates, whose numbers have surged in recent years. Mayor Bill de Blasio, in naming his correction commissioner, Joseph Ponte, said this month that the department had “sadly lagged behind other corrections systems.” He has vowed reforms.

Last week, news reports detailed the recent death of a mentally ill inmate who was left unattended for hours in an overheated cell on Rikers, where he was being held on a misdemeanor trespassing charge. Advocates for the mentally ill say that the deaths are emblematic of the neglect and indifference that are common at Rikers, the vast city jail complex in the East River, where violent encounters between inmates and guards have been on the rise in recent years.