The Apache helicopter crashed Monday in a residential area in Saga province, killing co-pilot Hiroki Takayama and leaving lead pilot Kenichi Saito missing.
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"We were informed that a body part was found. But we're still confirming the identity of the body part," a defence ministry spokesman told AFP.
The helicopter crashed in Saga prefecture seven minutes after takeoff, slamming into and setting on fire a house that was completely destroyed in the accident.
An 11-year-old girl was in the house at the time, but survived with minor injuries.
Video footage captured by a camera in a nearby car showed the helicopter dropping from the sky almost vertically, with its nose pointing directly towards the ground.
The crash site was just 300 metres (1,000 feet) from a local elementary school and sent a thick plume of grey smoke rising from in between the rooftops of local houses.
The AH-64 Apache attack helicopter was conducting a test flight after routine maintenance at the time of the accident, and had taken off from a Self-Defence Forces (SDF) base, according to the defence ministry.
Prime Minister Shinzo Abe offered said his government would investigate the incident.
"It is very regrettable that the Self-Defence Forces, which should protect the people's lives and peaceful living, threatened their safety and caused tremendous damage," he told a parliamentary session.
"I apologise sincerely," Abe added.
The defence ministry said it has suspended the flight of all 12 of its AH-64 helicopters for inspections.
The incident revived memories of a 2016 crash in which a Japanese air force jet with six people aboard went missing in mountainous terrain.
Their bodies were later recovered.
There has also been a string of accidents involving US military helicopters that have fuelled opposition to their presence in the country.
The latest was a UH-1 helicopter that was forced into an emergency landing last month on the southern Japanese island of Okinawa.
Japan's SDF have been banned from waging any kind of combat beyond defence of the nation since the US-imposed constitution of 1947 that followed the carnage of World War II.
But despite the limits on the scope of its military activity, Japan nonetheless boasts an impressive array of weaponry with highly trained personnel.
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