The head of Japan's National Police Agency announced his resignation on Thursday after an investigation into security for former prime minister Shinzo Abe, who was assassinated last month.

"We have decided to shake up our personnel and start afresh with our security duties, and that's why I tendered my resignation to the National Public Safety Commission today," Itaru Nakamura told reporters.

He made the announcement at a press conference detailing the findings of an investigation into flaws in how the former prime minister was protected.

"As we scrutinised and reflected on the incident, we decided to start over and overhaul our security system," Nakamura added.

Abe was shot and killed on the campaign trail on July 8 in the Nara region.

His suspected killer was detained at the scene and is believed to have targeted Abe because he thought he was linked to the Unification Church.

Abe was Japan's best-known politician and longest-serving prime minister, but security was comparatively light as he delivered a stump speech on a street in the western region.

Local police in the area have already acknowledged "undeniable" flaws in security for the former leader.