Efforts were on to fish out the two corpses, the official said.
The rescue operation was being carried out by Coast Guard personnel, police and members of a fishermen association, West Bengal Sundarbans Development Minister Manturam Pakhira earlier said.
The missing fishermen were travelling in five trawlers including two from Namkhana and three from Frazerganj.
Ten fishermen went missing from MV Joykishan and six others have gone missing from MV Malleshwar. Three other fishermen from some other trawlers also fell into the rough sea on Monday, the minister said.