City officials announced the measure Thursday, the New York Post reported.
"This is a problem across the country all of a sudden," Mayor Michael Bloomberg said at Elmhurst Hospital in Queens. "It's really on a lot of people's minds."
Dr. Thomas Farley said about 2 million prescriptions for opioid painkillers are written in New York each year. The city has a population of about 8 million.
"Make no mistake," Farley said. "These are dangerous drugs. It's best to think of them as heroin in pill form."
Before the new measure, emergency rooms dispensed seven-day supplies of painkillers, which Dr. Lewis Nelson said was excessive.
"Most acute pain -- from an ankle injury to a headache, whatever you'd like to pick -- lasts two to three days," he said.
The three-day supply rule is voluntary and doctors still have the discretion to prescribe what they feel is necessary on a case-by-case basis, the news report said.
"It's very hard to determine whether they're [patients] seeking drugs for their addiction or drugs for pain," Nelson said.