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TASS, which said the case was "top secret", identified the suspect as Baek Won Soon and said he had been detained in Russia's far-eastern city of Vladivostok.
It marks the first time Russia has arrested a South Korean citizen for criminal espionage, the agency said.
"According to a TASS source in law enforcement agencies, Baek Won Soon passed state secret information to foreign intelligence services," the agency said.
He was transported from Vladivostok to Moscow for further investigation and is being held in the capital's notorious Lefortovo prison, it added.
The prison, known for keeping detainees in near-total solitude, also currently houses U.S. reporter Evan Gershkovich, held on spying charges he denies.
Espionage carries a maximum jail term of 20 years in Russia.
Russia labelled South Korea an "unfriendly country" in 2022 after Seoul introduced sanctions against Moscow over its offensive in Ukraine.
The Kremlin has since forged closer economic and military ties with Seoul's arch-foe North Korea, a relationship that has caused unease in the South.
