Local media reports said three civil servants were hospitalised after being attacked by the furious crowd, but police said they were unable to confirm any injuries during Monday's protests.
"Officers were called in and we managed to bring the situation under control," police spokesman Prishantha Jayakody said. "A decision was then taken to distribute aid through cooperative stores rather than government offices."
More than a million people were temporarily displaced last week after heavy monsoon rains that claimed the lives of at least 43 people.
United Nations Deputy Emergency Relief Coordinator Catherine Bragg was due in Sri Lanka on Wednesday to launch an international appeal for funding and to supervise relief operations.
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The government's disaster management centre in Colombo said the number of people in state-run relief camps had dropped to 17,900 by Tuesday morning. Water levels have fallen across the island's flooded east and northern-central regions, but the weather office said