"We've found out that some system information such as IP addresses have been leaked and that's creepy enough," said a Mitsubishi Heavy spokesman.
"We can't rule out small possibilities of further information leakage but so far crucial data about our products or technologies have been kept safe," he said, adding the company first noticed the cyberattack on August 11.
A Japanese defense 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 U.S. defense 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.
It is the country's biggest defense contractor, winning 215 deals worth 260 billion yen ($3.4 billion) from Japan's Ministry of Defense 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 defense companies," Andrew Davies, a cyber-warfare analyst with the government backed defense 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)