FSB said the journalist for the Hokkaido Shimbun newspaper had been detained on Sakhalin Island in Russia's far east before he planned to leave the country, and was subsequently transferred to custody in Moscow, Interfax reported.
Russian state TV showed a man lying on a floor and handcuffed by three masked men in black uniform.
A voice behind the scene tells him he is suspected of spying.
TV also showed him boarding a plane accompanied by two FSB servicemen and then in a cage on trial at the Lefortovo district court in Moscow, which authorised his custody for nearly two months.
Russia regards Japan as an "unfriendly" country as it has joined international sanctions against Russia over the war in Ukraine.
Japan's embassy in Moscow did not answer phone calls out of business hours.
Russia and Japan never signed a formal World War II peace treaty, with the main obstacle being an unresolved territorial dispute over the Kuril Islands, known in Japan as the Northern Territories.
Russian President Vladimir Putin visited one of the disputed islands in August, causing an uproar in Japan.
Japan has said it would continue implementing sanctions against Russia and supporting Ukraine.
The Soviet Union took the Kuril Islands from Japan in the final days of World War II.
Russia has rejected Japan's complaints, reaffirming that Russia's "sovereignty and jurisdiction over the southern Kuril Islands are absolutely unshakable".
One of the most prominent cases of a foreign journalist arrested in Russia was the detention of Wall Street Journal reporter Evan Gershkovich in 2023.
He was found guilty of espionage by a Russian court, sentenced to 16 years and then freed in a prisoner swap in August 2024.
with AP
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