(Adds details from India)

DHAKA, Sept 23 (Reuters) - More than 100 Bangladeshi fishermen were missing after at least 15 fishing boats sank in a storm in the Bay of Bengal, witnesses and officials said on Sunday.

The Chittagong port authority issued an international maritime alert advising all ships and fishing boats to remain in shelters until further notice, said Syed Farhad Uddin, the secretary of Chittagong port.

Bangladesh's meteorological department said in a special weather bulletin that the monsoonal deep depression, which hit the Bay of Bengal on Thursday night, was moving north-north-west and had reached India's eastern coastal state of Orissa.

"Maritime ports of Chittagong, Cox's Bazar and Mongla have been advised to keep the local warning signal hoisted," the bulletin said.

The latest bulletin said the monsoonal low had crossed the Indian coast near Paradeep on Sunday and the weather system was now over Orissa and adjoining areas.

"It is likely to move in a north-north-westerly direction further inland and weaken gradually by giving precipitation," the bulletin said.

It said squally weather might affect the ports of Chittagong, Cox's Bazar and Mongla.

Flooding was reported in Orissa and the neighbouring state of West Bengal, forcing the evacuation of hundreds of people living in low-lying areas, including in the city of Kolkata.

In Orissa, three people died on Saturday after part of a house collapsed in heavy downpours in Cuttack, close to the state's capital, Bhubaneswar, where about a thousand people were affected.

Heavy seas were preventing rescue operations, but authorities said they would start a search as soon as the stormy weather subsided.

Surviving fishermen said they saw several boats sink. In Cox's Bazar, about 10 fishing boats with nearly 100 fishermen capsized. About 80 fishermen made it back to shore.

Officials also warned of flooding, with low-lying areas of several coastal districts, including Chittagong, Cox's Bazar and their offshore islands, likely to be inundated by water surges up to 4 feet (1.2 metres) high, driven by high winds.

Hundreds of Bangladeshi fishermen die and many go missing in storms in the Bay of Bengal every year. (Additional reporting by Nazimuddin Shyamol in Chittagong, Nurul Islam in Cox's Bazar, Bappa Majumdar in Kolkata and a Reuters reporter in Bhubaneswar)

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