The raids, conducted by the NYPD and Brooklyn District Attorney's Office, began at around 12:30 p.m.
Investigators planned to make arrests in up to 10 stores, mostly bodegas and delis, where clerks sold drugs from the counter.
In many cases, police say the owners were unaware that their clerks were dealing illegal drugs, many times to kids.
The raids are the culmination of an ongoing investigation into illegal drug sales on Nostrand Avenue, in the heart of Crown Heights.
Members of the community alerted officials with the DA's office to the pervasive marijuana sales.
Police Commissioner Ray Kelly and Brooklyn District Attorney Charles Hynes are overseeing the raids from a command post at the scene.