In a separate incident, also on Sunday, a policeman was shot dead in Dagestan, and another one was injured in an attack blamed on suspected separatist fighters.
Twin suicide bombings on Moscow's metro system on Monday killed at least 40 people and stoked fears of a campaign of attacks in by separatist fighters based in the North Caucasus region, which includes Dagestan.
Doku Umarov, the leader of the so-called Caucasus Emirate separatist group, claimed responsibility for the Moscow metro bombings.
Umarov has previously claimed responsibility for the bombing of a passenger train travelling between Moscow and St Petersburgin November, that killed 26 people.
A passenger train from the Siberian city of Tyumen to Baku was due to pass along the track where Sunday's blast took two hours after the cargo train was hit.
It was halted while the tracks were repaired, Interfax reported.
The main explosion was caused by a device equivalent to 5kg of TNT, while a "booby trap" device placed a few metres away contained the equivalent of one kilogram of TNT, an FSB spokesman was quoted as saying.
"The first results of an investigation started early Sunday suggest that this explosion is a continuation of a terrorist attack by North Caucasus rebels that began March 29," an unnamed official told RIA Novosti, apparently referring to the metro attacks.
There has been a surge in violent attacks across Russia's Caucasus region in recent months and Dmitry Medvedev, the Russian president, has vowed to hunt down and annihilate those behind the violence.
Chechnya in the North Caucasus has seen two wars and hundreds of violent attacks since the 1991 collapse of the Soviet Union.
Violence has spread from Chechnya to the neighbouring regions of Dagestan and Ingushetia.