It happened around 11 p.m. Tuesday at National Floral Design on Middle Country Road in Ridge.
Police say two men in their early 20s broke down the metal flag poles that stood on the side of the building and took the flags.
The flags represent the five branches of the military.
National Floral Design is a memorial florist for a national cemetery on eastern Long Island.
Anyone with information should call police or Crime Stoppers at 1-800-220-TIPS.