The incident took place last night when six persons, three each from Mariguda and Sanyasiguda villages, were returning from Andhra Pradesh after shopping.
According to Chitrakonda tehsildar Falguni Majhi, the six villagers from Kudmanur gram panchayat under Kalimela block, had gone to other side of the river for bringing some essentials like rice.
The boat capsized in mid-river leading to the missing of three persons belongng to Sanyasiguda village, he said.
Search operation is being carried with help of local fire brigade personnel and police men, he said.
The identity of the three missing villagers is yet to be established, the tehsildar said.