He said that the Liberation Tigers of Tamil Eelam (LTTE), an armed separatist group, was responsible for the attack.
The LTTE have not commented on the Sri Lankan military's allegations.
Packed train
Minelle Fernandes, Al Jazeera's correspondent in Colombo, said: "The kind of time we are looking at [for the attack] is workers going home after a hard day's work."
"The authorities are trying to get those injured rushed to hospital. This is not the first time that this station has been the scene of an attack.
"In 1996 there was a large attack at this station on a train carrying office workers. About 60 people were killed in that incident."
There have been several bombings against civilian and security targets in recent months.
Sri Lankan authorities have blamed most of the attacks on the LTTE, which is fighting for a separate homeland for ethnic Tamils.
Fighting has escalated in Sri Lanka since the start of the year, when the government pulled out of a truce with the LTTE.
Both sides say that each others' forces are targeting civilians - whether Tamil suicide attackers venturing into the south or army forces  operating inside the  rebel-held north.
Last week, the LTTE said that an army unit had killed 20 Tamil civilians in mine attacks in the north.