Shinya Yamada, 30, the third secretary at the Japanese embassy in Kinshasa, was arrested in Tokyo over allegations he set the blaze in June, police and reports said.
"It is extremely regrettable an official of the Foreign Ministry was arrested and that serious damage, including the loss of public funds, was inflicted," said Foreign Minister Fumio Kishida, adding an apology "to the people of Japan".
Yamada was a regular at local casinos in Kinshasa and frequently borrowed money from colleagues, the Nikkan Sports tabloid said.
Records of those entering and exiting the embassy building showed Yamada was the last person to leave on June 20, the day of the fire, the reports said.
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