The Japanese Navy's chief of staff quit on Friday after a raft of scandals including over people without adequate security clearances handling classified defence materials.

"I will resign from the chief of maritime staff job on July 19 and retire," said Admiral Ryo Sakai, the most senior uniformed officer in the Maritime Self-Defense Force (MSDF).

"As chief of the maritime staff, I am responsible for the training of personnel and the organisational management of the force, and I'm rightly held accountable for failing to fulfil my duties as the manager of specified secrets," Sakai told reporters.

Chief government spokesman Yoshimasa Hayashi also said that "disciplinary action" had also been taken against more than 200 people.

"The activities of the Self-Defense Forces are underpinned by the trust of the public, and these incidents, which must never be allowed to happen, are extremely regrettable," Hayashi told reporters.

"From now on, under the leadership of the defence minister, I hope that the ministry and the Self-Defense Forces will work together to ensure that measures are taken to prevent a recurrence of such an incident and that it never happens again," he said.

The defence ministry announced in April that five senior officers including a destroyer captain had been punished after an unvetted officer handled information on the location of other countries' ships.

Defence Minister Minoru Kihara said at the time that the material was not leaked to outsiders but that the government "takes these incidents extremely seriously".

It is just one of several controversies to rock Japan's military, which with US encouragement is being beefed up in response to China's growing assertiveness.

These include three Japanese soldiers sexually assaulting female colleague Rina Gonoi in 2021, whose complaints were initially brushed aside in an internal military probe.

The three men were convicted last year in a high-profile trial.