Myanmar’s recent political opening has unleashed deep-seated and violent ethnic clashes that have sent waves of refugees on perilous boat journeys to seek safer shores, while forcing its neighbors and international entities to scramble to come up with a cohesive response to the crisis. On New Year’s Day, authorities in Thailand intercepted 73 ethnic Rohingyas refugees fleeing their country. Thailand’s government says it has a policy of intercepting Rohingyas while still at sea and making sure they have enough fuel and supplies to sail to another country. But this time authorities repatriated the Rohingyas across the border to an uncertain future back in Myanmar despite the appeals from the United Nations High Commission for Refugees.

Elsewhere, Singapore’s Ministry of Home Affairs said Thursday the city-state doesn’t have the resources to absorb refugees. It recently refused permission for 49 shipwrecked people from Myanmar to come ashore there. “Opening our doors to refugees and asylum seekers would eventually pose serious social, economic and security problems for our small island state,” the ministry said.

Malaysia took in 40 survivors, while Indonesia took the other nine after appeals from the U.N. refugee agency and the ship’s Vietnamese owners.

On Friday, Indonesia’s Foreign Minister Marty Natalegawa said he would travel to Myanmar next week to examine conditions in Rakhine state at the invitation of the Myanmar government. He told journalists he would formally announce a pledge for $1 million in humanitarian aid to the region during his stay.

The bulk of these modern-day boat people are ethnic Rohingya Muslims. In Myanmar, they are denied citizenship in the Buddhist-dominated country, dismissed as being illegal migrants from Bangladesh despite many tracing their local roots back centuries. More than 100,000 are estimated to have fled their homes in the state, where they make up about a quarter of the population.

Malaysia, which is predominantly Muslim, has done more than most countries to bring the Rohingyas’ plight to international attention. About 25,000 Rohingyas are registered as refugees there, according to the United Nations, while others live there illegally.

A spokesman at Malaysia’s Ministry of Foreign Affairs says it cooperates with the UNHCR and other international organizations to handle refugees and asylum seekers on a case-by-case basis, and, like Indonesia, is urging Myanmar authorities to eradicate the root cases of the violence in western Myanmar and prevent a greater exodus.

Even so, Malaysia also appears nervous about the growing numbers of refugees trying to make their way to the country. The illegal refugees risk whipping, among other punishments, if they are caught by immigration authorities.

Recently, many Rohingya Muslims in Myanmar have been forced into refugee camps following clashes with local Buddhists that resulted in more than 170 deaths last year in Rakhine state. Once in the camps, aid agencies complain about local Buddhist militias making it difficult to deliver food and medicine to the more than 100,000 people crammed into tents and dilapidated dormitories.

Conflict analysts estimate that thousands are paying up to $300 each to board creaking trawlers and tug-pulled barges to make the voyage south. Few countries, however, are prepared to absorb them.

“We’re trying to urge all the governments in the region to allow the migrants to land so that we can determine their status and see whether they need international protection,” said Babar Baloch, a spokesman for the UNHCR, in Geneva, which is attempting to forge a coordinated response to the migrations.

Regional leaders at the Association of Southeast Asian Nations have tried to address the problem, realizing the extent to which the controversy could hurt the trade bloc’s image, especially in the Muslim world.

Cracks in Asean between Buddhist-majority countries such as Thailand, Myanmar and Cambodia, and predominantly Muslim nations such as Indonesia and Malaysia, could widen, making a coherent strategy harder to reach, said Yang Razali Kassim, of the S. Rajaratnam School of International Studies at Singapore’s Nanyang Technological University. “There are growing signs of agitation, especially within the Muslim communities of Southeast Asia, at the seeming lack of peace efforts.”

The group generally steers clear of interfering in its member states’ internal affairs, but Asean officials have urged Myanmar and Bangladesh to recognize Rohingyas as citizens and to provide more incentives for them to stay in Myanmar.

Thailand’s foreign ministry also said Myanmar is responsible for stemming the outflow of refugees. Indonesian presidential spokesman Teuku Faizasyah said Indonesia viewed a resolution to the communal conflict in Rakhine state an essential component tackling the root causes of the Rohingya refugee problem.

The Myanmar government has set up an inquiry into the causes of the violence.

Malaysia remains a preferred destination. Many Rohingyas in Myanmar who are mulling the voyage, such as Aung Soe from the riot-torn town of Kyauk-Phyu, say they have relatives who have made the voyage there, helping to provide a support network for new immigrants.”Malaysia is the best place for us to go, if we can get there,” Mr. Aung Soe, 27 years old, said shortly after the recent violence in Rakhine state, looking out at a small flotilla of battered fishing boats anchored a few miles south of Sittwe, the area’s main port. “I already have two cousins working there.”

Those who do make it provide a valuable financial lifeline for their families left behind. “Without my son in Malaysia, I don’t know how I would be able to survive,” said Kyaw Hla Aung in a recent interview in Takebi, Myanmar, one of the fetid refugee camps in the baking-hot delta of the Kaladan River.

The risks don’t end when the voyagers enter Malaysian waters, however. On Dec. 30, around 450 Rohingyas, including women and children, leaped into the sea off the coast of the island of Langkawi from a rickety fishing boat and swam their way to shore where they were detained by waiting immigration officials. One person died, killed by the boat’s propeller. Malaysian officials didn’t respond to requests to comment.

More Rohingyas appear set to risk their lives to make the voyage. “We’re seeing more and more boats leaving, especially after Bangladesh tightened its border controls. Now people are willing to go further to escape the conditions in the refugee camps in Rakhine State,” said Mr. Baloch at the UNHCR.

—Celine Fernandez in Kuala Lumpur and Ben Otto in Jakarta contributed to this article.
Write to James Hookway at