The incident was reported at 338 Court St. just after 4:30 p.m. on Wednesday.
A partial stop work order had been issued for failure to maintain the building and it appears to have been under construction.
The building housed a gym called Body Elite on the first floor.
In June, the gym posted a message on Facebook to its members that it was undergoing an exterior makeover while it was closed due to COVID-19.
It is not yet clear if there were any injuries, but the FDNY says all workers have been accounted for.
Video posted to social media shows the immediate aftermath of the collapse:
The FDNY has pulled all members from conducting searches due to the possibility of a secondary collapse.
The NYPD asked residents to avoid Court Street between Atlantic Avenue and 1st Place and Union Street from Henry Street to Smith Street.
FDNY responds to 3-story building collapse in Brooklyn