The RIA-Novosti news agency also quoted several passengers as saying that they heard a loud bang immediately before the derailment.
Investigators were trying to determine the cause of the explosion, Pirkov said.
A statement posted later on the Russian Railways website said the derailment was due to "illegal interference in the operations of railway transportation".
In all, 12 cars and a locomotive of the "Nevsky Express" derailed. The train was carrying 215 passengers and 20 crew members at the time, Pirkov said.
All traffic along the Moscow-St Petersburg route - one of the busiest for the Russian Railways network and popular with foreign tourists - was halted.
The Interfax news agency, citing an unnamed law enforcement official, said investigators had found a 1.5m-by-1.5m crater under the train's ninth car.
One passenger told NTV by telephone that some people appeared trapped in the cars, with conductors, train workers and other passengers smashing windows to try to help people as downed power lines crackled overhead.