A small fire scorched the "Gate of gods", which stands about 13 metres (43 feet) tall and 28 metres wide, at around 4:00 am, the official said.
The gate, built in 1934 and adorned with huge gold-leaf chrysanthemums on both portals, was not seriously damaged as a shrine security guard quickly put the blaze out, she said.
"We believe it was arson because our security footage shows somebody spraying liquid on the gate before the fire started," she said.
Police later found two glass containers that appeared to have contained some kind of fuel oil, local media said.
Japanese media reported that a posting on Twitter, apparently by a Korean resident of Japan, had threatened a fire at the shrine.
However, a Tokyo police spokesman played down the speculation.
"We are aware of such an Internet posting before the incident," he said.
"But we see threats against the emperor or the prime minister posted on the Internet everyday. We investigate all such cases."
The Yasukuni shrine is a Shinto sanctuary dedicated to 2.5 million Japanese killed in wars, including 14 of Japan`s top World War II criminals.
It is regularly a source of friction with Japan`s neighbours --
particularly China and South Korea -- who say it honours those responsible for terrible crimes.
(U.C003)
Editor: Priyambodo RH
Copyright © ANTARA 2011
