Television footage showed a ball of fire roaring towards the minister, Jeyaraj Fernandopulle, as he signalled the start of the race. KA Karunarathne, a former top marathon runner, was among the dead.
About 100 people, some of them runners in the race, were wounded.
Mr Fernandopulle, 55, was a member of the government negotiating team for failed peace talks with the Tamil Tiger rebels two years ago.
Authorities immediately blamed the Liberation Tigers of Tamil Eelam (LTTE).
Mr Fernandopulle was the second minister to be killed since January.
The minister for nation building, DM Dassanayake, died in a roadside blast in the same district, Gampaha.
The Sri Lankan military has launched an offensive on the LTTE's northern strongholds in which at least 100 rebel fighters were killed last week, according to the military.
The rebels have in the past hit back with bombings in Colombo and in the relatively peaceful south of the island when they have come under military pressure in the north and east.
The attack took place in the town of Weliveriya, 30 km from Colombo.
A number of Irish volunteers based in Sri Lanka are reported to be safe and well following the attack.
The attack claimed the lives of 12 people including a government minister.
The Irish volunteers are working with the Partners in Care Charity, which is based in Cork.
The volunteers are based in the town of Weliveriya, close to where the attack took place.
