The bombs were planted on the track of the railway line linking Kislovodsk to Mineralnye Vody in the Caucasus region. There were about 50 people in the third car of the six-car train which was directly hit by the blast, Railway Ministry's spokesman Konstantin Pashkov said.
Each bomb contained about 150 grams of explosives and the two blasts killed five people, Russian officials said.
Nikolai Lityuk, a deputy chief of the Emergency Situations Ministry in southern Russia, said up to 30 people were wounded in the explosion which occurred as the train was approaching a station in the town of Podkumok.
No group immediately claimed responsibility for the blasts.
Viktor Kazantsev, President Vladimir Putin's envoy to southern Russia, told state television that police had arrested a man suspected of detonating the bombs.
Russia has been rocked recently by numerous bombings and other attacks, which the government usually blames on the Chechen rebels.
An officer at the headquarters of the Caucasus Military District, which oversees Chechnya, said on condition he not be identified that the military had received intelligence information that the rebels were preparing a series of attacks in southern Russia.
The explosion occurred just as Putin was scheduled to chair a meeting of regional governors in Rostov-on-Don, some 280 miles northwest of the explosion site.