China's increased economic and military powers, along with its growing influence in Asia, have raised tensions between the two countries.
The helicopter at the centre of the investigation is the R-MAX, which can be flown safely by a relatively untrained operator on the ground just using a laptop computer.
The Ministry of Trade and Industry says Yamaha should have sought official permission before exporting the helicopters to China.
Yamaha were surprised by the investigation and denied doing anything wrong. The firm claimed they had first sold the helicopters to China five years ago and said that they were basic models that could have no military use.
The company has also promoted the aircraft as being of use for surveillance, and this is probably what has sparked the concerns.
The helicopters have been used for crop spraying so it could be assumed they could also be used in biological and chemical warfare. About 1,600 R-MAX helicopters are currently in use in Japan, and farmers are mainly using them.
Yamaha admit to having sold nine of the helicopters to China in the past.