A boat carrying up to 150 Rohingya Muslims fleeing a cyclone has capsized off Myanmar's coast, the UN said Tuesday, as the storm threatened to strike flood-prone Rakhine State over coming days.

The boat went missing on Monday night after it left Pauktaw township, a spokeswoman for the UN Office for the Coordination of Humanitarian Affairs said, adding there were an unknown number of missing as "they were travelling to another camp ahead of the cyclone".

About 140,000 people displaced by communal violence last year are living in flimsy tents or makeshift housing across Rakhine prompting fears that they are vulnerable to cyclone Mahasen, which was gathering strength in the Bay of Bengal.

The cyclone is expected to make landfall somewhere near the Myanmar-Bangladesh border on Thursday night, according to an update by Myanmar's Department of Meteorology and Hydrology.

Local officials said Myanmar's army had been deployed in preparation for the cyclone and to help relocate thousands of displaced people living in low-lying coastal areas.

The IDPs (internally displaced persons) at particular risk are mostly stateless Rohingya Muslims uprooted by two outbreaks of deadly religious violence since June last year.