The suspects had tried to use one of Russia's most powerful supercomputers to mine Bitcoins, media reports say.
The Federal Nuclear Centre in Sarov, western Russia, is a restricted area.
The centre's press service said: "There has been an unsanctioned attempt to use computer facilities for private purposes including so-called mining."
The supercomputer was not supposed to be connected to the internet - to prevent intrusion - and once the scientists attempted to do so, the nuclear centre's security department was alerted. They were handed over to the Federal Security Service (FSB), the Russian news service Mash says.
"As far as we are aware, a criminal case has been launched against them," the press service told Interfax news agency.
Crypto-currencies like Bitcoin do not rely on centralised computer servers. People who provide computer processing power to the crypto-currency system, to enable transactions to take place, can get rewards in Bitcoins.