A second, less powerful bomb exploded at 2:00pm (11:00 GMT) on Saturday near the site of the first blast, though no one was injured, the head of Russia's state railway operator said.
Vladimir Yakunin, the president of Russian Railways, also said that the accident may have been caused by an explosion under the tracks.
"There is objective evidence that ... a blast from an explosive device is one of the explanations for the Nevsky Express incident," he said.
Russia's prosecutor general has opened a criminal case on terrorism charges, Russian news agencies have reported.
Al Jazeera's Neave Barker, reporting from Moscow, said that the attack has broad implications for safety protocols across Russia's rail network.
Al Jazeera's Jonah Hull reports on the Russian authorities investigation into deadly train crash
"It was an organised attack deliberately designed to target the Nebsky express on a Friday evening, perhaps one of the busiest time of the week when travellers, commuters, tourists were going through Russia's two biggest cities," he said.
"Before the train derailed, officials on the ground had said there was a metre-wide crater very close to the site of the wreckage and also on Russian television, a recorded interview with the driver of the train which he believed that a bomb had been detonated underneath his train on his journey from Moscow to St Petersburg."
Our correspondent said there are deep concerns that Friday's incident is an act similar to what happened a few years ago involving the same line and train service.
A bomb blast in 2007 derailed a passenger train and injured about 30 people.
"It's still very early to suggest who was behind the attack, but officials have drawn comparison to a similar incident two years ago when a bomb was detonated under the same service and derailed 12 out of 14 carriages of that train. There were no deaths, but at least 30 people were injured," Barker said.
"Two suspects were arrested and they are believed to have been from Ingushetia with possible links to fighters operating across the Caucasus region."
The country's anti-terrorism committee has sent units to the area to help with the rescue effort and the investigation, Interfax news agency reported.
Dmitry Medvedev, the Russian president, ordered Bortnikov, the head of the FSB domestic security service, and Prosecutor General Yuri Chaika to lead the investigation into the causes of the derailment, the Kremlin said in a statement.
|Investigators suggest the derailment was caused by an act of terrorism [AFP]
Dimitry Babich, an analyst for Russia Profile
magazine in Moscow, told Al Jazeera: "Officials from the Federal Security Service (FSB) are saying that there was an explosive device that used seven kilos of TNT.
"That's a substantial amount and now we can be pretty sure that the disaster was caused by a terrorist attack."
Attacks are relatively frequent across Russia's North Caucasus, and include the December 2003 suicide bombing of a train near Chechnya that killed 44 people.
The last fatal attacks outside the volatile southern region, however, occurred in 2004 with the twin bombings of passenger aircraft that killed more than 80 people.
Those attacks were blamed on Chechen rebels, as were the February 2004 Moscow metro bombings that killed 40 people.
The 2007 derailment of a train on the Moscow-St Petersburg line was caused by an explosion and injured 27 people. Authorities have arrested two suspects and are searching for a third - a former military officer.
Another train derailment in June 2005 left at least 12 injured. The train had been travelling from Chechnya to Moscow.