National Police Agency Chief Itaru Nakamura's announcement came as his agency released a report blaming flaws in police protection of former prime minister Shinzo Abe, who was shot and killed on July 8.
The head of Japan's National Police Agency has announced his resignation after an investigation confirmed "shortcomings" in the security plans for assassinated former prime minister Shinzo Abe.
Abe, the country's best-known politician and longest-serving premier, was shot and killed while delivering a stump speech on July 8 in the city of Nara in western Japan.
"There were shortcomings in the security plans and the risk assessments on which they were based, and direction from the field commander was insufficient," Itaru Nakamura told reporters on Thursday.
"The root of this problem lies in the limitations of the current system, which has been in place for years, in which local police bear sole responsibility for providing security."
Nakamura said he would take responsibility for the failings and step down from his post as police chief.
"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," he said.
Nakamura did not say when his resignation would be official. Japanese media reported that his resignation is expected to be approved at Friday's Cabinet meeting.
In a 54-page investigative report released on Thursday, the National Police Agency concluded that the protection plan for Abe neglected potential danger coming from behind him and merely focused on risks during his movement from the site of his speech to his vehicle.
Inadequacies in the command system, communication among several key police officials, as well as their attention in areas behind Abe at the campaign site led to their lack of attention on the suspect's movement until it was too late.
None of the officers assigned to immediate protection of Abe caught the suspect until he was already seven metres behind him where he took out his homemade double-barrel gun, which resembled a camera with a long lens, to blast his first shot that narrowly missed Abe. Up to that moment, none of the officers was aware of the suspect's presence, the report said.
In just over two seconds, the suspect was only 5.3 metres behind Abe to fire the second shot.
The report said the prefectural police's Abe protection plan lacked a thorough safety evaluation. It called for significant strengthening in both training and staffing of Japan's dignitary protection, as well as revising police protection guidelines for the first time in about 30 years.
The national police called for doubling dignitary protection staff, greater supervisory role for the national police over prefectural staff, and use of digital technology and drones to bolster surveillance from above ground.