The shooting happened around 4 p.m. along Linden Boulevard Pennsylvania Avenue.
Police said the officer was shot while driving in the parking lot of the Mcdonald's.
The officer was taken to Kings County Hospital. Her condition was not immediately released, but the injuries were described as not life-threatening.
The gunmen remained at large.
A large number of police vehicles remained on the scene looking for them, and for clues as to what happened.
COP SHOT has posted a $10,000 cash reward for information on the suspect(s) who allegedly shot the off-duty police officer in East New York.
Anyone with information about the shooting should call the organization's toll-free hotline, 1-800-COP-SHOT. All information will be kept strictly confidential. No names are taken and callers are issued an identification number.