The Investigative Committee said that the suspects are residents of the former Soviet Central Asia region like the bomber, 22-year-old Akbarzhon Dzhalilov, a native of Kyrgyzstan.
The impoverished, predominantly Muslim countries in Central Asia are seen as fertile ground for Islamic extremists, and thousands of their residents are believed to have joined the Islamic State group in Syria and Iraq.
The committee, the nation's top criminal investigation agency, said investigators also found objects that would help advance the probe during a search of the home on St Petersburg's eastern outskirts.
The building's residents had been evacuated before explosives experts went in to check the site. Konstantin Serov, the chief administrator in the city district where the building is located, told Russian news agencies that police deactivated an explosive device at the apartment.
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Police in the city are on high alert following Monday's explosion that killed the attacker and 13 other people and wounded some 55.
Today's arrest came a day after law enforcement agencies detained eight Central Asian migrants suspected of acting as recruiters for the Islamic State group and al-Qaida's Syria branch. The investigators found no immediate evidence of their involvement in the subway attack.