Animal-welfare advocates had filed a lawsuit against East Hampton over its plan to thin the herd.
The New York Times that both the village and town of East Hampton decided Friday to withdraw from the plan.
The goal of the federally funded sharpshooter program was to eliminate 2,000 to 3,000 deer this year from a population officials have put at 25,000 to 35,000.
Long Island's deer have caused car accidents and Lyme disease, which is borne by deer ticks. They also eat crops and landscaping.
East Hampton Village Administrator Becky Molinaro says the village will look at alternatives including sterilization.