The recent violence in Burma's Rakhine state makes it even more unlikely that they can return.
The Rakhine Buddhists and Muslims, believed to be mainly Rohingya, blame each other for the violence.
The U.N. humanitarian office held emergency meetings in Yangon and Sittwe, the capital of Rakhine state, over the weekend.
Officials said there were no new reports of violence since Friday and that they have restored order in Rakhine.
President Thein Sein declared a state of emergency in Rakhine on 10 June.
The estimated 45, 000 refugees living in Sittwe, Pauktaw, Myebon and Kyauktaw in Rakhine state are the "most vulnerable, " it added.
Three people have been killed in clashes between Muslims and Buddhists in the western Burmese state of Rakhine, officials say.
Muslims and Rakhine Buddhists blame each other for the violence, reports say.
In comparison, all of Rakhine state, she said, is "highly vulnerable, " even if it isn't where the cyclone first makes landfall, because of inadequate infrastructure.
This separation of communities is now seen across Rakhine, he adds.
"It's all over, and we are very relieved that we didn't have any unfortunate incident in Rakhine state due to the cyclone, " regional spokesman Win Myaing said.
The impending rains, which mark the start of Myanmar's monsoon season, underscore the urgency for the country's government to get a handle on sectarian tensions in Rakhine state.
Tensions in Rakhine state have remained high since those clashes.
"We are assuming these are the people from the boat from Pauktaw, Rakhine that capsized on Monday night because none of the locals here have reported anyone missing, " he said.
State broadcasters on Monday said over 5, 000 people have been relocated from the flood-prone areas around Sittwe, the capital of Rakhine, to safer districts less vulnerable to storm surges or landslides.
U.N. agencies are working with the Rakhine state government, planning for strong winds, expected to be 80 kilometers an hour or more, and are identifying communities that are most at risk.
Despite recent "positive developments" in Burma - including the release of political prisoners and an outline peace agreement with Karen rebels - the UK said there were "ongoing challenges", particularly the conflict in Rakhine state, where 100, 000 people have been displaced.
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