The FSB did not name the scientist, who it said had carried out distributed denial-of-service (DDoS) attacks on critical infrastructure on behalf of Ukrainian security services.
The domestic security agency said that the scientist had also sent money to the Ukrainian military, as well as gathered information on the Russian armed forces. The suspect had confessed, it said.
It was not immediately clear when the arrest was made. Russian media outlets published what they said was footage of the scientist's detention.
The video, which shows a man arrested in a snow-covered city, suggested that the scientist may have been detained some time ago.
Ostorozhno Novosti, a Telegram channel that covers Russian politics, identified the scientist as Artyom Khoroshilov, a physicist who state news agency RIA previously reported was arrested on suspicion of staging DDoS attacks in December 2023.