More than 30 people of at least 60 injured were hospitalized after the train derailed at 9:38 p.m. Moscow time (5:38 p.m. GMT).
Anti-terrorist measures will be carried out in the Nizhny Novgorod Region in central Russia, a source said.
Anastasia Popova, spokesperson for the Tyumen department of the Sverdlovskaya railway in West Siberia, said security had been tightened on local railways.
"Security on railway facilities and in places where large numbers of people gather has been increased," she said.
Reinforced police patrols have been dispatched to key railway facilities and passenger and commuter trains in the North-Caucasus railway in southern Russia.
Nikolai Kovalyov, head of the committee for veterans' affairs at the State Duma and former chief of the Russian Federal Security Service (FSB), said last night's accident could be connected to a military operation in Ingushetia, a troubled republic in the North Caucasus, where almost 2,500 Interior Ministry officers have been deployed to fight militants.
"That could have been an attempt to divert attention to another location - a method frequently used by terrorists," Kovalev said in an interview with RIA Novosti. "Or else there could be quite a trivial explanation of boys playing war games."
His opinion was shared by Gennady Gudkov, a member of the security committee at the lower house of Russia's parliament, who said the explosion could be a reaction to an anti-terror operation in Ingushetia.
However, Mikhail Grishankov, first deputy chairman of the State Duma security committee, said it was too early to speculate.
"That was a strange crime, and it is too early and complicated to discuss it. We should wait for the expert report," he said.
Meanwhile, the first commuter train traveled along the repaired track at 3:50 p.m. (11:50 a.m. GMT). Traffic is currently running to schedule.
The latest reports said the Zhaso insurance company promised to pay everyone injured in the train crash up to 12,000 rubles ($471) depending on the severity of injuries.
A Zhaso insurance payment of over 2 rubles ($0.09) is included in the cost of all railway tickets.
The Russian Railways monopoly has said a terrorist attack was the only possible explanation, but law enforcement authorities are considering several other versions, including technical failure.