Indonesia and Thailand also appeared unwilling to provide refuge to men, women and children, despite appeals by the UN High Commissioner for Refugees, international aid agencies and rights activists, who warned lives were at risk.
Fearing arrests, captains tied to trafficking networks have in recent days abandoned ships in the busy Malacca Strait and surrounding waters, leaving behind their human cargo, in many cases with little food or water, according to survivors.
Malaysian Deputy Home Minister Wan Junaidi said about 500 people on board a boat found Wednesday off the coast of northern Penang state - three days after more than a thousand refugees landed on nearby Langkawi island were given provisions and then sent on their way.
"What do you expect us to do?" he said. "We have been very nice to the people who broke into our border. We have treated them humanely but they cannot be flooding our shores like this."
"We have to send the right message that they are not welcome here," he said.
Southeast Asia, which for years tried to quietly ignore the plight of Myanmar's 1.3 million Rohingya, now finds itself caught in a spiraling humanitarian crisis that in many ways it helped create.
In the last three years, more than 120,000 members of the Muslim minority have boarded ships to flee to other countries, according to the UN refugee agency.
But no governments in the region appear willing to take them in, fearing that accepting a few would result in an unstoppable flow of poor, uneducated migrants.
Denied citizenship by national law, members of the Rohingya minority are effectively stateless. They have limited access to education or adequate health care and cannot move around freely.
They have been attacked by the military and chased from their homes and land by extremist Buddhist mobs.
With the crisis now reaching a crescendo, Thailand said it would hold an emergency meeting later this month in Bangkok to discuss the exodus and "root causes." Representatives from 15 countries, including the US and Australia, are expected to attend.
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