BBC News reported the company as saying that eight viruses were found on 45 servers and 38 computer terminals last month.
The viruses targeted a shipyard in Nagasaki, a facility in Kobe and a plant in Nagoya, where the company designs and builds destroyers, submarines, guidance and propulsion systems for rockets and missiles respectively.
The Japanese Defence Ministry has said that the attackers failed to access sensitive information, however, it has ordered the company to carry out a full investigation.
Japanese Defence Minister Yasuo Ichikawa said, “The ministry will continue to monitor the problem and conduct investigations if necessary.”
An ongoing internal investigation conducted by the company found only network information, such as IP addresses were compromised.
Japanese Government websites, the Cabinet Office and a video distribution service were also hit by distributed denial-of-service attacks.