Japanese police have arrested a South Korean man suspected of bombing Tokyo's controversial Yasukuni shrine, local media said.

A small blast hit a public toilet on 23 November as the shrine opened for a festival. There were no injuries.

The suspect, 27, is alleged to have gone to Korea after the incident, but was arrested on his return to Japan.

The shrine is dedicated to Japan's war dead including some convicted war criminals.

The souls of the dead are worshipped there rather than just remembered, making visits to it by conservative politicians like current Prime Minister Shinzo Abe, particularly controversial with World War Two adversaries China and the two Koreas.

READ MORE: Tokyo's Yasukuni shrine hit by blast in toilets

The visits are seen as a lack of remorse on Japan's part for its militaristic past.

Public broadcaster NHK said police approached the man at Tokyo's Haneda airport and arrested him on a charge of illegal entry into the shrine. The man denies the allegation according to NHK.

Japanese media had previously identified the suspect from CCTV footage from the shrine and the nearby area, where he is reported to have stayed.

The shrine was busier than usual on the morning of the blast. Photo: Reuters

The blast reportedly opened a hole in the ceiling and left behind the remains of batteries, wires and metal pipes that police believe contained explosives.

It is not the first time the shrine has been attacked.

In 2011, a Chinese man is suspected to have set fire to one of the gates of the shrine, although a court in South Korea - where he served time in jail for a 2012 attack on the Japanese embassy in Seoul - refused to extradite him to Japan.

And in 2013 a South Korean man was caught breaking in to the shrine carrying a bottle of paint thinners, which he was then reported to have thrown at the main hall.