The vehicle was peppered with shrapnel, suggesting a powerful fragmentation mine placed on the roadside had been detonated as the bus was passing, the agency said.
On Wednesday, 18 people were wounded when a bomb exploded on a rail track as a train bound for Colombo was passing through a southern suburb of the city.
Last week, an explosion inside a train on the same track killed nine people and wounded 84.
All the attacks have been blamed on the Tamil Tigers who are under pressure from the military which is advancing on their strongholds in the northern Wanni region.
Updated It was the second bomb attack in the capital this week believed to have been carried out by the Tamil Tigers and comes in the wake of an attack last week that killed nine people.
Police curfew has been imposed in Katubedda area in