The corpse was discovered on Wednesday inside a former housing area at Camp Foster but the identity of the person, including their gender and approximate date of death, were unknown, a spokeswoman for the base said.
The United States Naval Criminal Investigative Service is leading a probe into the case, she added.
The body was badly decomposed, but was presumed to be that of an adult, said an official at Okinawa prefectural police headquarters.
Okinawa is host to nearly half of the 47,000 US service personnel in Japan, with large tracts of land on the island chain taken up by bases and military housing complexes.