"One can say with certainty that it was an act of terror," Vladimir Markin, a spokesman for the investigative committee of the Russian prosecutor's office, told CNN .
Markin said investigators had discovered "elements of an explosive device" that left a crater beneath the railroad bed, but would not elaborate.
The high-speed Moscow-St. Petersburg Nevsky Express, carrying 681 people, derailed Friday night about 174 miles from St. Petersburg.
Russian Interior Minister Rashid Nurgaliyev said investigators have been focusing on possible suspects, including a stocky, middle-aged man with red hair.
But authorities did not offer specifics on who might have have been responsible for the bombing.
Federal Security Service Director Alexander Bortnikov said experts have concluded the explosive device contained the equivalent of about 15 pounds of TNT.
Earlier this decade, Russia had been targeted by terrorist attacks carried out by separatists from the Muslim region of Chechnya, but the attacks had subsided in recent years outside Caucasus, The New York Times reported. But the Times said authorities investigating the bombing appeared to be focusing on Muslim extremists or Russian ultra-nationalists.
Eighteen passengers who were thought to have been on the train remained unaccounted for Sunday.
A law enforcement source told CNN some body parts may not have been identified yet; some injured passengers may have left the scene of the wreck before rescuers arrived; and some people whose names appeared on the passenger list may have bought tickets but never boarded the train.