Police say Dr. Franck Leveille was supposed to examine the victim at the Rose M. Singer Center at the time of the alleged incident in March 2010.
Authorities began investigating an allegation of prohibited sexual contact between an inmate and a facility doctor. Under New York law, an inmate in a correctional facility is legally incapable of consenting to sexual activity with an employee or contractor providing services to inmates at the facility.
Leveille, 60, was arrested Wednesday morning at his office in Brooklyn.
According to the criminal complaint, at about 2 a.m. on March 28, 2010, Dr. Leveille touched a female inmate without her consent and engaged the inmate in a criminal sexual act without her consent.
When the allegation was reported, Dr. Leveille was immediately removed from inmate contact and has been assigned since then to administrative duties.
The doctor has been licensed as a physician in New York State since 1993 and has been employed on Rikers Island since January 1998.
"This physician is charged with exploiting an inmate in his care, according to the criminal complaint, and violating his fundamental professional responsibility," Department of Investigations Commissioner Rose Gill Hearn said.
Dr. Leveille, of Rockville Center, has been charged with criminal sexual act and sexual abuse. He faces up to 4 1/3 years in prison if convicted.