Russia’s security service says a terrorist bomb derailed a busy high-speed train and killed at least 26 people on Friday night.

Federal Security Service officers briefed Russia’s president Dmitri Medvedev yesterday on the attack, just hours before a second, less powerful, bomb exploded on Saturday at the site of the train derailment.

Russian Railways chief Vladimir Yakunin said no one was injured in the second blast yesterday, at 2pm local time near the site of the original explosion, which officials said caused a luxury express train en route from Moscow to St Petersburg to career off the tracks.

Yesterday it was reported that investigators had found traces of explosives among the wreckage of the train derailed on Friday, leading to widespread suspicion that the explosion was the work of terrorists.

Russian news agencies yesterday quoted Alexander Borotnikov, head of Russia’s domestic intelligence service, as saying that a home-made bomb had been detonated, derailing the express train on Friday night.

At least three of the 14 carriages left the tracks as the train reportedly approached speeds of 130mph.

“Criminology experts say, on the basis of preliminary information, that an improvised explosive device, equivalent to 7kg (15 lb) of TNT, had gone off,” said Mr Bortnikov.

The full death toll is still unclear. The Health Ministry says 26 people were killed, but prosecutors estimate at least 30. Emergencies Minister Sergei Shoigu was told by a ministry official on a video conference shown live on Vesti-24 state television that the death toll had risen to 39 after more bodies were pulled from wrecked carriages. Up to 100 people have also been reported injured. Some eyewitness reports described a 3ft wide crater next to the railway track.

The train, known as the Nevsky Express, was carrying 661 passengers from Russia’s capital to its second city. It was derailed at 9:34 pm local time on Friday near the village of Uglovka, about 200 miles north of Moscow.

The train was travelling on one of the busiest rail routes in Russia, and Friday evening is peak travel time.Soldiers were seen carrying four body bags away from the scene. Rescue workers cut through the tangled steel to search for survivors trapped in and beneath wrecked train carriages.

“There is objective evidence that … a blast from an explosive device is one of the explanations for the Nevsky Express incident,” Russian Railways chief Vladimir Yakunin told reporters at the scene.

Russian television channels broadcast a recording of a mobile phone call from the train driver to the emergencies ministry.

“There was an explosion under the locomotive,” he said. “I do not know what we hit. We are derailed – the locomotive and carriages, I do not know yet what else – everything is in smoke. “

The derailment is Russia’s worst train disaster for years and talk of sabotage is likely to raise fears of an upsurge in attacks on the Russian heartland by rebels from the North Caucasus.

After a blast in August 2007 on the same line derailed the Nevsky Express and injured at least 30 people, prosecutors arrested two men suspected of having links to Chechen rebels and charged them with helping to carry out the attack.

Russian prosecutors said they believed ex-soldier Pavel Kosolapov, a former associate of the late Chechen rebel leader Shamil Basayev, was the mastermind behind the blast. Kosolapov is still on the run.

In Washington, White House spokesman Robert Gibbs said: “We are deeply saddened by the terrible loss of life and injuries resulting from the reported derailment of a train between Moscow and St Petersburg.”

Though no group has yet claimed responsibility for Friday’s attack, Pavel Felgenhauer, defence correspondent for Russia’s Novaya Gazeta newspaper, said the key suspects would be “either militants from Russia’s North Caucasus region or nationalist extremist, pro-Nazi groups”.