Japan's prime minister on Tuesday called on the US military to suspend helicopter operations in the country's southern Okinawa island chain after a fatal crash.

An American HH-60 helicopter with four personnel on board crashed at the Camp Hansen Marine base on Monday.

Three of the crew were rescued. A fourth was missing but search operations were called off after human remains were discovered at the fiery crash site, the US Air Force said in a statement Tuesday.

"The remains have yet to be identified," it added.

On Monday, a Japanese defence ministry official had said the fourth crew member was taken to hospital, but the information was later updated.

"I conveyed my regrets over the accident to the US side and strongly asked them to take preventative measures, share information and pursue the cause of the accident," premier Shinzo Abe told reporters.

"I asked (the United States) to suspend, for now, the operation of the same types of helicopters as the one that crashed."

The base is located on Okinawa, which is home to tens of thousands of US military personnel, with the latest incident stoking renewed concerns among many residents about the vast American presence there.

"In our village, residential areas are located next to exercise zones and we had fears about a crash," said Atsushi Touma, head of a village near the Camp Hansen base.

Okinawans have mounted protests against both the US military and its deployment of the controversial Osprey aircraft on the island.

Local media reported that about 200 people on Tuesday staged a fresh rally near the gates of Futenma Air Base, where the Osprey aircraft has been based, shouting in chorus: "US bases must be removed."

The Osprey is a hybrid aircraft with rotors that allow it to take off like a helicopter and engines that can tilt forward, enabling it to fly like an airplane at greater speed than a chopper.

It has been plagued with safety problems although the US military insists such glitches have been fixed.