
Some information may have been leaked in the incident in September with an organised attacker such as a nation state "strongly" suspected, Kyodo News agency reported, citing unnamed ministry sources.
"It is a very serious situation. We must quickly take measures to prevent a recurrence," one unnamed military official told Kyodo.
The full scope of the damage is not clear, Kyodo said.
A Defence Ministry spokesman denied the report.
The Defence Information Infrastructure, a high-speed large-capacity communication network connecting military bases and camps, was subject to the attack, the report said.
The hacker was reportedly able to gain unauthorized access to computers at the National Defence Academy and the National Defence Medical College, using them as a gateway to enter the computer system.