The Interfax news agency reported Monday that authorities think the bomber was linked to radical Islamic groups and carried the explosive device onto the train in a backpack.
Russian investigators said they had detained several suspected accomplices of Akbarzhon Jalilov, born in mainly Muslim Kyrgyzstan, who is the suspected bomber in Monday's metro blast.
Investigators said Djalilov - believed to be a Russian citizen born in the Central Asian nation of Kyrgyzstan - had set off a bomb in a train carriage travelling between two busy Saint Petersburg metro stations on Monday afternoon.
Seven suspected IS recruiters have been arrested by authorities investigating the explosion, but officials found no immediate evidence of their involvement in the attack. The attack happened while President Vladimir Putin was on a visit to Russia's second-largest city, which is also his native town. Numerous attacks were linked to radical Islamists. Fifty-five people wounded in the blast remain hospitalized, deputy mayor Anna Mityanina said Wednesday.
Dmitry Peskov told reporters on Tuesday that the fact that Putin was in the city when the bomb went off, although several dozen miles away from where he was hosting talks, "makes one pause" and is "something for the intelligence agencies to analyze".
A search of the suspects' homes had turned up objects that were important for the investigation, it said. Speaking to Reuters, the security source said, "Explosives were in a similar amount that was used at Vosstaniya (metro station)".
Churches across the city held prayers for victims killed in the attack, including Irina Medyantseva, a 50-year-old artist who was locally famous for the dolls she made and sold.
Monday's blast between two stations killed 14 people and injured nearly 50.
The subway system in St. Petersburg, a city of 5 million that typically is crowded during peak commute hours, looked nearly deserted on Tuesday as many residents opted for buses.
"The conclusions of the genetic examination and the recording of the CCTV cameras give the investigators reasons to believe that it was Dzhalilov who committed the terrorist act in the train", said the RIC in a statement.
There has been no claim of responsibility.
Jalilov allegedly detonated an explosive on the city's metro between the central Sennaya Square and Tekhnologichesky Institut stations.