A Japanese military helicopter has crashed into a house in south-western Japan, killing one of its two crew members and ripping the top floor off the house and setting it on fire, officials said.

The other crew member was missing and one resident of the house was injured.

The Boeing AH-64 Apache helicopter, belonging to the Ground Self-Defence Force's Metabaru training camp, crashed in Kanzaki city in Saga prefecture seven minutes after taking off on a test flight after routine maintenance, defence officials said.

The Defence Ministry said the co-pilot suffered heart and lung failure and was later pronounced dead, and the pilot was missing.

The ministry earlier said both had been found.

A AH-64D helicopter - the same model that crashed into the house. ( AP: Japan Ground Self-Defence Force )

Public broadcaster NHK showed orange flames and black smoke rising from the charred house.

Witnesses reported a big boom and ripping noises from the sky before the crash.

An 11-year-old girl was the only one of the four residents of the damaged house who was home at the time, and managed to escape, according to Saga prefecture's disaster department.

It said she suffered a minor knee injury.

The house next door and a storage building were also damaged, the disaster department said.

Defence Minister Itsunori Onodera said the helicopter fell nose-first after losing contact with air traffic control.

He said the cause of the accident was under investigation.

Prime Minister Shinzo Abe ordered the grounding of all 12 helicopters of the same type for safety checks, Kyodo News agency reported.

The crash followed a series of emergency landings and other incidents involving US military aircraft on Japan's southern island of Okinawa.

AP