Mitsubishi Heavy Industries said on Monday its computers had been hacked into, with one newspaper saying the target was Japan's biggest defence contractor's factories for submarines, missiles and nuclear power plant components.
A Mitsubishi Heavy spokesman said information could have been stolen in what was the first known cyber attack on Japan's defence industry.
A Japanese defence white paper released last month urged vigilance against cyber attacks after a spate of high-profile online assaults this year that included Lockheed Martin and other US defence contractors.
There were suggestions at the time that those attacks had originated in China.
The Yomiuri newspaper said about 80 virus-infected computers were found at the company's Tokyo headquarters as well as manufacturing and research and development sites including Kobe Shipyard & Machinery Works, Nagasaki Shipyard & Machinery Works and Nagoya Guidance & Propulsion System Works.
Kobe Shipyard currently builds submarines and makes components to build nuclear power stations, while the Nagasaki Shipyard makes escort ships.
The Nagoya plant makes guided missiles and rocket engines, the paper said citing unnamed sources.
At least eight different kinds of computer virus including Trojan horse, which steals key information from infected computer hardware, were found at Mitsubishi Heavy's main office or production sites, the Yomiuri said.
The company said in a statement that the viruses were discovered in mid-August and reported to authorities.
It denied that product or technology information had been leaked externally by the viruses.
It also said that it had taken "measures to prevent the spread of damage", including by installing anti-virus software and by continuing investigations.
Mitsubishi Heavy Industries is the country's biggest defence contractor, winning 215 deals worth 260 billion yen ($US3.4 billion) from Japan's Ministry of Defence in the year to last March, or nearly a quarter of the ministry's spending that year.
Weapons included surface-to-air Patriot missiles and AIM-7 Sparrow air-to-air missiles.
Mitsubishi Heavy has also been working closely with Boeing, making wings for its 787 Dreamliner jets.
"It's probably just the first that hacking attacks in Japan have been detected. It's consistent with what we've seen already with big American defence companies," Andrew Davies, a cyber-warfare analyst with the government backed defence think-tank, the Australian Strategic Policy Institute, told Reuters.
"The Japanese make large conventional submarines that are among the world's most sophisticated ... (they) have very nicely integrated solutions with their own mechanical, electronic and control systems, so it a pretty attractive hacking proposition, to get the design of a Japanese submarine," he added.
($1 = 76.875 Japanese Yen)
(Additional by Rob Taylor in Canberra, Editing by Jonathan Thatcher)