Shinya Yamada, 30, the third secretary at the embassy in Kinshasa, was arrested earlier this month in Tokyo over allegations he set the blaze in June.
Tokyo prosecutors indicted Yamada on charges that he had poured gasoline on offices at the premises and then set light to them.
Yamada told police he was trying to destroy the mission to cover up the fact that he had embezzled embassy money, local reports have said.
Police believe he had taken embassy money to fuel his gambling habit and the arson was his bid to remove evidence of his crime.