Rescuers were on Tuesday searching for 58 missing Rohingya Muslims whose boat capsized in western Myanmar as they fled a looming cyclone, state media said, as the storm threatened thousands living in makeshift camps.

The boat, which sank after hitting rocks in a coastal waterway on Monday night, was one of seven vessels carrying Rohingya seeking out higher ground from a camp in Pauktaw township in Rakhine state, according to state television.

"The rescue operation is ongoing because 58 people are still missing," it said, adding that 42 people had been rescued.

Cyclone Mahasen has prompted mass evacuations in Rakhine, where about 140,000 people, mainly Rohingya, are living in flimsy tents or makeshift housing after two waves of deadly communal violence between Buddhists and Muslims last year.

Myanmar's department of meteorology on Tuesday said the cyclone was travelling through the Bay of Bengal about 510 miles (820 kilometres) from the state capital Sittwe with wind speeds of about 60 miles (100 kilometres) per hour and would make landfall on Thursday near the Myanmar-Bangladesh border.

It threatens to worsen the humanitarian crisis in Rakhine, which was sparked by two outbreaks of deadly religious violence beginning last June that saw around 200 people killed and the homes of tens of thousands razed.

In Geneva a spokesman for the UN's refugee agency said millions of people living in the area could be hit, with latest estimates suggesting some 69,000 displaced people in three locations were at particular risk.

An update from ASEAN's disaster relief arm said the Pauktaw camps housed 17,000 displaced people and were "particularly vulnerable", adding that camps sited on rice paddies would be swamped by any storm surge.

Fear of the impending storm has spread through the makeshift camps.

"We are holding prayers at the camp not to be hit by the cyclone. We have suffered so much already," Maung Maung, a Rohingya at Thechaung camp near Sittwe told AFP.

He said the authorities had given information and some assistance, but added it was not enough. "We are still living under the rain," he said.

Some Rohingya have reportedly refused to leave their shelters in a sign of the festering mistrust of their ethnic Rakhine neighbours and of security forces.

"We do not want to move to another place in this weather," said another Rohingya Muslim near Sittwe, also named Maung Maung.

"We are better off staying here to die."

Myanmar's army was deployed to help evacuate those most at risk. But some international observers said the effort had come too late after months of warnings of the danger posed to the camps by this year's monsoon.

"If the government fails to evacuate those at risk, any disaster that results will not be natural but man-made," said Brad Adams, Asia director at Human Rights Watch.

The warnings have revived memories of Cyclone Nargis, which devastated Myanmar's Irrawaddy Delta in May 2008 and killed about 140,000 people.

Bangladeshi authorities have warned that the cyclone could barrel into coastal homes there, but have so far stopped short of issuing an evacuation order for residents in the low-lying Chittagong area, home to some 30 million people.

The Muslim nation is also home to a large, longstanding Rohingya refugee population, estimated at around 300,000, with many living in cramped coastal camps just over the border from Rakhine.

An official from Bangladesh's Cox's Bazaar district, the site of a number of such camps, said authorities were using loudspeakers to warn islanders and coastal dwellers of the storm.

Thousands of Rohingya have fled Myanmar in rickety and overcrowded boats since the Rakhine violence erupted. Scores have died making the perilous journey south towards Thailand and Malaysia.

Myanmar views its population of roughly 800,000 Rohingya as illegal Bangladeshi immigrants and denies them citizenship.