Vladimir Yakunin, the head of Russian Railways, did not mix words on a statement he made on state television, standing next to the wreck.
"To put it simply, a terrorist attack", he said.
Several other sources have suggested it may have been the result of an explosion.
News agencies cited unidentified officials as saying a 1-metre crater was found at the site of the wreck.
"One of the versions is that the cause of the incident was an explosive blast," Russian Railways said in a statement.
Some Russian news agencies quoted transport officials as saying the electricity supply might have been at fault.
The country's anti-terrorism committee dispatched units to the area to help with the rescue effort and the investigation, Interfax news agency reported.
Dmitry Medvedev, the Russian president, ordered Alexander 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.
"Two wagons were completely overturned ... Several people were completely crushed under the metal. I heard screams, moaning," Andrei Abramenko, a passenger on the train, told Vesti 24 television.
Al Jazeera's Neave Barker reporting from Moscow said some eyewitnesses mentioned hearing a loud explosion and authorities said they are not ruling out terrorism.
Our correspondent said there are deep concerns that Friday's incident is a repeated act of terrorism similar to what happened a few years ago involving the same line and train service.
A bomb blast on the same line derailed a passenger train and injured about 30 people in 2007.
The line between Russia's capital and its number two city is heavily travelled and trains are often crowded.