While the major motorcycle maker denied any wrongdoing, police and customs mobilized 280 investigators to search 20 locations, including the company's head office in Iwata city southwest of Tokyo.
The probe comes amid growing friction between Japan and China, in part over wartime memories and scarce energy resources.
Yamaha had tried to send the helicopter via Hong Kong to a Beijing-based company with deep ties to China's People's Liberation Army, Jiji Press news agency said, quoting investigatory sources.
The news sent the stock of Yamaha tumbling 235 yen or 8.08 percent to end at 2,670 yen on the Tokyo Stock Exchange.
Chief Cabinet Secretary Shinzo Abe said the case was "very regrettable."
"We hope the investigation will reveal the full extent of the case," Abe, the top spokesman of the government, told reporters.
Yamaha Motor allegedly tried to export one helicopter to China in December without due permission from the trade minister although the machine is subject to export control, police said.
The trade ministry filed a criminal complaint with police against Yamaha Motor and its president Takashi Kajikawa for alleged violation of foreign trade control law.
If found guilty of illegal exports, they are punishable with imprisonment of a maximum five years and a fine of up to two million yen (17,500 dollars).
The RMAX series of unmanned helicopter, which flies at low altitudes of up to 150 meters (500 feet), is used to discharge agricultural chemicals in Japan.
As the model boasts of high performance and is equipped with the satellite-based Global Positioning System, it could be converted to spread germs if equipped with biological weapons, reports said.
Yamaha defended its actions, saying it exported nine units of the model to an aerial photographing company based in Beijing over several years but that only the attempted 10th export triggered the raids.
"We do not recognize at all (that we were) engaging in acts that violate laws," Toyoo Otsubo, Yamaha Motor's director in charge of public relations, told a nationally televised news conference in Iwata city.
He said the company did not believe the helicopter in question could be converted to military use.
Public broadcaster NHK said the locations raided by police included a Chinese-run trading company in Tokyo that allegedly brokered the deals.
Jiji Press reported that police had been led to the case when they searched the company in April last year on suspicion of it having brought in illegal immigrants from China.