What is behind the measure is unclear.
According to information in the Japanese media, however, the man has stated that he opposes plans to hold a state funeral for former Prime Minister Shinzo Abe, who was assassinated last summer.
A police officer who tried to put out the fire is said to have been injured.
Abe was shot dead in connection with an election rally on July 8 and the state-funded funeral is scheduled for September 27.
However, state funerals are not common in Japan and the decision is controversial. According to opinion polls, around half of Japanese oppose the plans.