Close relatives waited in vain on the seashore for the trawlers to return - but survivors said they had seen many of their colleagues battling the high walls of water.
Sources in the southern port city of Chittagong confirmed the return of 200 fishermen with their trawlers late Wednesday as the winds eased.
Fisheries ministry officials said the untraced fishermen were on board the trawlers which were badly battered by tropical gales stirring high waves in the Bay which have flooded at least seven coastal districts.
About 100,000 rice farmers living on the fragile coastline fled their mud-baked homes by Wednesday as tidal surges battered rice fields, destroyed road links and dealt a heavy blow to forests and rural power supply networks.
The central office of disaster management said about 2,000 fishermen were reported missing in inclement weather in the southern Bangladesh district of Barguna.
Rescue workers claimed at least 15 fishermen were drowned in thunderstorms after their boats sank in rising walls of water off the Barguna coast.
Another 1,000 fishermen were reported missing in Cox's Bazar district and an estimated 500 more were feared drowned in the area near the islands of Maheshkhali and Saint Martins off the southern coast.
"The fishing trawlers apparently moved into deep sea in search of a bigger catch, ignoring warnings of rough weather," said a fisheries ministry official on condition of anonymity.
The search and rescue operation has been intensified by coast guards and the fishermen's association in the southern Patuakhali town which lies under knee-deep water.
The Met Office said high tide flooding was intensified by the gravitational pull of the full moon and a series of mild tremors which rocked central and southern parts of Bangladesh, setting off panic.
Earlier reports said nearly 50,000 people were driven from mudflat villages by the flooding as local rivers burst banks while the situation was exacerbated by thunderstorms.
Surging waters have triggered cracks in river dams, washed away shrimp farms and forced the evacuation of at least a thousand families to highlands from their fragile homes in the worst affected Noakhali district, said local civilian administrator Imamuddin Kabir.
At least 40 Bangladeshi trawlers with 240 fishermen aboard, which were caught in the elements and driven off course, have sought refuge in neighbouring West Bengal coast in India. dpa af jh sc
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