A resident wait near the area after an explosion at a subway station in St Petersburg, Russia on April 3, 2017. [Photo/VCG]

Interfax cited an unidentified law enforcement official saying that investigators think the suspected suicide bomber left the bomb at the Vosstaniya Square station before blowing himself up on the train.

The agency said authorities believe the suspect, a 23-year old who came from ex-Soviet Central Asia and was linked to radical Islamist groups, carried the explosive device onto the train in a rucksack.

Asked about the report, Putin spokesman Dmitry Peskov wouldn't comment, saying it's up to law enforcement agencies to comment on details of the probe.

The entire St Petersburg subway system was shut down and evacuated, but partial service resumed after about six hours.

Security was immediately tightened at all of the country's key transportation sites, Russia's National Anti-Terrorist Committee said. Moscow officials said that included the subway in the Russian capital.

Putin, who meeting with the president of Belarus at the Constantine Palace on the city's outskirts, offered condolences on national television.

"Law enforcement agencies and intelligence services are doing their best to establish the cause and give a full picture of what happened," a somber-looking Putin said.

He later laid flowers outside the Technological Institute station, where the damaged train arrived after the explosion.

Some residents of St. Petersburg, a city of 5 million, responded with both dismay and determination.

"They won't succeed in breaking up our country. We are all citizens of one country despite various political views and religious beliefs," said 24-year-old Alexander Malikov, who brought flowers and candles to an improvised memorial outside one of the stations.