"All those injured were in the second carriage behind the engine," Jayawardene said.
Wave of attacks
The wounded were rushed to nearby hospitals, Gunasekera said.
The bomb, which weighed around 5kg, had been laid on a stretch of track parallel to where the train was passing, police commandos at the scene told AFP.
Colombo has been hit by a string of recent bombings, with officials blaming the Liberation Tigers of Tamil Eelam (LTTE).
Last month, a bomb aboard a crowded commuter train killed 11 people during the evening rush-hour just outside Colombo.
Sri Lanka's defence ministry did not say who was responsible for Wednesday's attack.