Dr. Stan Li already had been accused of prescribing prescription drugs to addicts.
Li prescribed more than 500 pills to a 21-year-old man in the five weeks leading up the discovery of his body in a parked car in Queens in 2010, authorities said. The cause of death was acute intoxication caused by a combination of Xanax and oxycodone.
Authorities said they believe it's the first time a physician has been charged in New York with manslaughter in an overdose death.
"Dr. Li flouted the fundamental principle in medicine - first, do no harm," Special Narcotics Prosecutor Bridget Brennan said in a statement announcing the indictment.
Li, of Hamilton, N.J., was to appear in court later Thursday. There was no immediate response to a message left with his attorney.
The 58-year-old Li has previously pleaded not guilty to peddling prescriptions to addicts and drug dealers from a Queens weekend clinic where he saw as many as 120 patients a day, moonlighting from his full-time job as an anesthesiologist at a New Jersey hospital.
One of Li's patients, David Laffer, shot and killed two employees and two customers while holding up a Long Island pharmacy for painkillers in June 2011. Authorities have said that Li provided 24 prescriptions filled by Laffer.
Laffer is serving a life sentence for murder.