A man who claims to be a member of a right-wing organization threw a smoke marker at the Chinese Consulate General in Nagasaki City on Sunday.
Police officers guarding the facility at the time arrested 20-year-old part-time worker Kazuki Tanigawa.
No one was injured as the office was closed for the weekend.
Police say more officers were deployed than usual following the release of the captain of a Chinese fishing boat that collided with Japanese Coast Guard vessels near the Senkaku Islands.
US Ambassador to Japan John Roos is also visiting the city.