Reuters said an emergency service source has told them there was one blast that took place between two stations.
Earlier the agency reported that blasts took place in two train carriages at two stations and Russian news agencies also reported two blasts.
The Reuters source said the explosion occurred as the train was travelling between Sennaya Ploshchad and Technology Institute stations.
Authorities gave no other immediate details on the investigation. Russian news agencies said a second explosive device was found that did not detonate.