A Tokyo shrine seen as a symbol of Japan's past militarism on Monday reported a second case of graffiti in three months.

The Yasukuni shrine in Tokyo honours 2.5 million mostly Japanese killed in wars since the late 19th century, including convicted war criminals.

Officials regularly pay homage at Yasukuni, as did three government ministers and scores of other lawmakers on the 79th anniversary of Japan's surrender in World War II on Thursday.

Such visits have angered some of Japan's Asian neighbours and former victims of its imperialism, especially China and South Korea.

A Yasukuni shrine official confirmed the new case of graffiti to reporters, without elaborating further.

In late May, a Chinese man allegedly conspired with two others to spray-paint the word "toilet" in red on a pillar at the shrine.

Jiang Zhuojun, 29, who lived north of Tokyo, was later arrested "on suspicion of vandalism and disrespect for a place of worship", Tokyo police said in July. (AFP)