DHAKA, BANGLADESH - Two children drowned, about 400 fishermen were missing and thousands of people were marooned after storm-whipped waves from the Bay of Bengal swept Bangladesh's vast coastline, officials said on Wednesday.

Sea water flooded at least two towns - Patuakhali and part of Cox's Bazar - forcing many residents to flee as others huddled in their homes braving strong wind and heavy rain.

Weather officials said the sea surge was triggered by a "depression" in the northern Bay, likely to persist for a couple of days before crossing India's Orissa coast.

"The Bay has been very rough since Monday, when dozens of boats managed to return to the shores, but about 400 others are still unaccounted for," one fisherman said.

Tidal waves spawned by the storm have inundated Patuakhali town and dozens of islands along the coasts, officials and weather monitors said.

Ports have been asked to hoist distant warning signals while fishing trawlers and ships were advised to come back or stay close to the shore.

The flooding also damaged hundreds of homes, crops and fish farms, local officials said, without giving any estimate of losses.

The sea waves struck while much of the country was still reeling under monsoon floods that have killed at least 20 people in the country's northeastern areas over the past month.

The deluge made thousands homeless and have caused water-borne diseases in the affected areas.

Bangladesh, home to more than 140 million people, faces frequent floods and storms that claim hundreds of lives every year, and leave millions homeless.

In November last year, Cyclone Sidr killed over 3,300 people and destroyed homes, crops and infrastructure worth billions of dollars on a vast swathe of coastal area.