As part of the camp, the cadets were taken for trekking through different routes daily and today they went to the Mahagony Forest Plantation at Moolamkuzhi near the river, a senior NCC official said.
The boys went into the river to click photographs and were caught in the whirlpool moments after which they drowned, Lt Col Madhusoodanan, Administrative Officer, NCC, who was in the camp, told PTI.
"There are standing orders in all NCC camps not to go to the water bodies. The boys were also told not to get into the water. But they said they are just going to click some photographs", he said.
The deceased were identified as Hemant (15), a school student, Mohammed Dishan (19), Sabeesh Baqri (19), Dilshad Alam (18) and Gulvez Ahamed (18)-- college students.
An inquiry has been ordered into the incident, a Defence press release said.
A pall of gloom descended on the camp following the incident.
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Police sources had earlier stated that the mishap occurred when the cadets had gone for a bath in the river.
Over 1000 NCC cadets from across the country have congregated at Malayattoor for the 8-day national level trekking camp which began on December 23.
The camp was being organised by the Ernakulam NCC Group of Kerala NCC Directorate.
Defence minister A K Antony expressed his anguish at the tragedy.