The Myanmar government had planned to move some 38,000 internally displaced people, most of them Rohingya Muslims, who have complained of severe abuse at the hands of the Burmese Army.
Authorities in Myanmar struggled on Wednesday to evacuate tens of thousands of people, most of them Rohingya Muslims, before a cyclone reaches camps in low-lying regions that have been their home since ethnic and religious unrest last year.
The Myanmar government had planned to move 38,000 internally displaced people, most of them Rohingya Muslims, by Tuesday but many have refused to relocate from camps in Rakhine State in the west of the country, afraid of the authorities' intentions.
At least 192 people were killed in June and October last year in violence between ethnic Rakhine Buddhists and Rohingya, who are denied citizenship by the government in Myanmar and considered by many Buddhists to be immigrants from Bangladesh.
At a camp near the sea by Hmanzi Junction on the outskirts of Sittwe, the capital of Rakhine State, several people told Reuters they would rather perish in the storm than evacuate.
"We arrived here last year because of the clashes between Rakhine and Muslims. I lost everything. Both my mother and my two young daughters died," said Hla Maung, a Muslim.
"If the cyclone hits here, I will pray to Allah. Everyone here wants to die in the storm because we lost everything last year."
The UN Office for Coordination of Humanitarian Affairs, which is helping Myanmar's government in Rakhine State, said the storm appeared to have weakened but could still threaten 8.2 million people in northeast India, Bangladesh and Myanmar.
There are up to 250,000 Rohingya living in southern Bangladesh, many of whom fled from Myanmar in the early 1990s complaining of abuses by the army.
The UN refugee agency said about 40,000 Rohingyas in Bangladesh were living in two unofficial sites and the government had given an assurance that everyone would get help.
Authorities in Bangladesh started moving people out of low-lying areas on the coast as the storm approached to within 800 km (500 miles). It was likely to intensify and bring a storm surge of up to 2.1 metres (7 feet), authorities said.
The port in the Bangladeshi city of Chittagong and the airport in Cox's Bazar were closed on Wednesday.
The evacuations in Myanmar are seen as a test of the government's willingness to help the Rohingya, an impoverished, long-persecuted people who bore the brunt of sectarian violence in Rakhine State and suffered before that during half a century of military rule.
Hla Maung and others had rejected efforts by the UN refugee agency on Tuesday to move them to a nearby army barracks. They were told early on Wednesday they could take shelter in a school, but many still refused to go.
Most of the people in the camp had lived in Thandawli, a village in the Sittwe region destroyed in last June's violence.
About 140,000 people were displaced in June and a second wave of violence in October.
Even before the storm developed, the United Nations has said about 69,000, most of them Rohingya Muslims, were living in Rakhine State in accommodation at risk of flooding and other damage during the rainy season, which starts this month.
It warned last week there could be a humanitarian catastrophe if people were not evacuated.
One of a small convoy of boats carrying Rohingya Muslims capsized at around midnight on Monday after hitting rocks off Pauktaw in Rakhine State. Official media said 42 people had been rescued but 58 were missing. Some reports have said eight bodies were found.
Speaking at a coordination meeting for Cyclone Mahasen in Yangon on Tuesday, President Thein Sein urged officials to use the experience gained in 2008 after Cyclone Nargis killed up to 140,000 people in the Irrawaddy Delta, south of the main city, Yangon. He stressed the need to treat everyone equally.
"Security, safety, food, and health care are crucial. And it's very important to carry out relief work on humanitarian grounds for all regardless of race and religion," official papers quoted him as saying.
Myanmar is a mainly Buddhist country but about 5 percent of its 60 million people are Muslims. They face a growing anti-Muslim campaign led by radical Buddhist monks and a Reuters Special Report found apartheid-like policies were segregating Muslims from Buddhists in Rakhine State.
(Additional reporting by Aung Hla Tun in YANGON, Ruma Paul in DHAKA; Writing by Alan Raybould; Editing by Robert Birsel)