Nair along with the others were taking part in a temple festival, "Valla Sadya', a celebration of the Sree Parthasarathy Temple near here.
Speaking to IANS, an official attached to the Aranmula Police station confirmed that Nair was in the snake boat.
"The boat capsized and immediate rescue services was undertaken and managed to rescue all passengers, while two are still missing," said the official.
Nair, who hails from the state, plays for Karnataka and was in the recent Indian team which toured Zimbabwe.