Most of the children were relatives and neighbours and have come here for a vacation when the tragedy struck them at Changrakkulam this evening.
A total of nine persons were onboard the small craft for a pleasure trip in the backwaters.
Two children and the boat's oarsman had been rescued by police and local people and hospitalised, Ponnani Circle Inspector Sunny Chacko told PTI.
The bodies of four girls and two boys, aged between four and 18, had been recovered, police said.
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The State Human Rights Commission has suo motu registered a case and ordered a probe into the incident.
A commission press release said the District Collector and police chief had been asked to file a report within three weeks.
Kerala Assembly speaker P Sreeramakrishnan, who represents the Ponnani constituency, in a statement condoled the death of the children and said the incident was very painful.