The trawlers from Kochi port were engaged in deep-sea fishing about 100 nautical miles off Karwar coast on Tuesday when the incident occurred, official sources said.
However, there was no human casualty as the fishermen from other boats sailing in the vicinity rescued the fishermen onboard the three trawlers.
Cyclone Phyan, which prompted Met department to issue warning on Tuesday to people along the western coast, caused story conditions, turning the sea very rough and bringing heavy rains in many places in the three coastal districts of Karwar, Udupi and Dakshina Kannada.
Besides the sinking three trawlers, the rough sea also damaged a barge, laden with nearly 800 tonnes of manganese ore worth Rs 45 lakh.
On receiving distress calls from the troubled barrage, some fishermen rescued nine workers onboard in a three-hour operation, said officials.
At least 10 boats on the Tagore beach at Karwar were also damaged. Several boats were found floating on the sea as their anchors had broken into pieces.
Standing paddy crops along the coasts as the sea water gushed into the paddy fields in Poojageri and Gabitawada the standing crops were damaged.
There were also reports of damage to at least six boats in Kundapur, Malpe and Shiroor.
A boat with three Tamil fishermen has gone missing. The boat had left Ullal on November 7, according to police sources. The boat was supposed to return on November 9. However, on November 9, the three fishermen called up the boat owner and said that the boat was 35 nautical miles away from the shore and its engine had developed some technical problem.
Meanwhile, heavy rain continued to lash Dakshina Kannada and Udupi districts on Wednesday. Thunder storm and lightning claimed one life in Bantwal taluk. The deceased, Narayana Nayak (52), was a resident of Kallangala, near Vittal town.