The incident took place just south of the capital Colombo in Buttala, police said, adding that the injured had been taken to nearby hospitals for treatment.
"Two females and a 12-year-old child were among the victims killed when LTTE (Liberation Tigers of Tamil Eelam) terrorists opened fire at the civilian bus," the ministry said.
The fourth victim died shortly after admission to hospital.
In January, 25 people died when Tamil Tiger rebels set off a roadside mine in the same area, hitting a crowded passenger bus.
Sri Lanka's rebels have been waging a war against the government since 1972 to carve out a separate homeland for minority Tamils in the island's north and east. Fighting is currently centred around the north, but the rebels routinely carry out attacks against military, economic and civilian targets elsewhere on the island.
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