The Japan Times said the search of the Maritime Self-Defense Force's First Service School in Hiroshima Prefecture was conducted Saturday and was the first by authorities of a military installation over possible violation of the 1954 law governing military secrets.
Personal computers were seized by authorities as well as administrative registers and other materials, reports said.
Additional details of the search were not disclosed, but the raid was part of an ongoing effort to trace the source of leaked data that ended up in the hands of several MSDF personnel.
The leak embarrassed the Japanese government, which is pursuing closer cooperation with the United States in ballistic missile defense, information sharing and military force cooperation.
Washington has reportedly expressed concern to Tokyo over the information leak.
The leak of data -- including training information on how to operate the system -- was discovered in March when authorities searched the home of an MSDF petty officer and found the material on a computer. Early reports said police had raided the home because the man's wife -- of Chinese origin -- was suspected of espionage. Other reports suggested the secret information was apparently downloaded from a computer when sailors were sharing downloaded pornographic images.