Moscow's FSB security service said a Japanese national was arrested on the Far East island of Sakhalin, near a disputed cluster of islands, but did not name the individual.
Tokyo summoned the Russian ambassador on Wednesday to lodge a protest over Moscow's arrest of a Japanese journalist on suspicion of espionage, with the foreign ministry urging "fair and impartial treatment."
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Russia has arrested several citizens of what it calls "unfriendly" countries in recent years, accusing them of working for Western intelligence services.
Russia's foreign ministry identified the reporter as Yuki Imai from the Hokkaido Shimbun newspaper on Tuesday, with a spokesperson saying he was accused of "conducting espionage activities on Russian territory."
Moscow's FSB security service said a Japanese national was arrested on the Far East island of Sakhalin, near a disputed cluster of islands, but did not name the individual.
It said the person had worked for Japanese intelligence to collect information about Russia's defences.
On Wednesday, the Japanese foreign ministry said European Affairs Bureau official Kimitake Nakamura summoned the Russian ambassador, Nikolay Nozdrev.
Nakamura "lodged a strong protest with the Russian side over the detention of a Japanese national and the issuance of unilateral statements regarding the case", the ministry said in a statement.
It added that Tokyo had not received any explanation concerning the case.
Kremlin spokesperson Dmitri Peskov meanwhile said in a briefing that the security service "is doing its job."
"If there are spies, they get caught," he said.
Chief Cabinet Secretary Minoru Kihara said Japan has not been able to contact the individual and did not know about the arrest until the official announcement from Moscow.
Japanese diplomats in Russia have requested "the prompt provision of information" and "humanitarian consideration and fair and impartial treatment," Foreign Minister Toshimitsu Motegi said.
The Hokkaido Shimbun said in a statement that it was aware of the Russian announcement but was "still confirming the details."
"Ensuring the safety of the journalist is our top priority and we are responding accordingly," the newspaper said.
Territorial dispute
The FSB said it had "opened a criminal case against the Japanese national" and that he had been placed in pre-trial detention, TASS and RIA Novosti news agencies reported, citing the security service.
Russian media reported he would remain in custody until 12 December.
"Attempts by Tokyo to use its correspondents in Russia...to gather information aimed at undermining the security of our state is regrettable," Russian foreign ministry spokeswoman Maria Zakharova said.
This was "not an isolated case," she added.
The charges carry up to 20 years in prison.
Media rights group Reporters Without Borders (RSF) called for the journalist's "rights to be respected and for his release," saying in a statement on X that the gathering of information is part of journalism.
The FSB published a video showing masked officers storming a hotel room, pushing a man to the floor and handcuffing him.
He was flown to Moscow, where a court ordered he be held in pre-trial detention.
It did not say when the arrest or court hearing occurred.