The remains were found in a lot near Maple and Main streets in Bay Shore. Detectives say two people walking to the nearby Fire Island ferry discovered the body shortly before 7 a.m.
A law enforcement source tells NBC 4 New York the woman's legs had been partly cut off.
It wasn't clear how long the body was in the lot before it was found, and investigators wouldn't say whether the woman was killed there or somewhere else.
The medical examiner will conduct an autopsy to determine how the woman died.