Police say the officer was in the third floor apartment on Clarendon Road when he accidentally fired his weapon just before 8 a.m.
The shot went through the floor and struck a 25-year-old woman in an apartment below.
The woman is a Japanese tourist.
She was rushed to Kings County Hospital in stable condition. The victim was treated and released for a graze wound to her arm.
The officer, assigned to Brooklyn South Narcotics, was not injured.
He was part of a group searching the apartment during a routine drug raid. Two people were taken into custody, and officers reportedly found narcotics, possibly crack cocaine.
Police carried the woman's luggage out of the apartment and gave her a full escort to the airport and her trip home to try and make up for the scare.
Get Eyewitness News Delivered