There were conflicting statements on whether regional governments would continue to push back migrant boats in the face of the UN warning that they risked a "massive humanitarian crisis".
"Indonesia, Malaysia and Thailand have decided not to receive boat people, as far as I am aware," Major General Werachon Sukhondhapatipak, spokesman for Thailand's ruling junta, told Reuters.
He declined to comment on the UN refugee agency UNHCR's appeal on Tuesday for an international search and rescue operation for the many stranded on the seas between Thailand, Malaysia and Indonesia.
"If these three countries move forward with push backs, blood will be on their hands."
The UN has said several thousand migrants were abandoned at sea by smugglers following a Thai government crackdown on human trafficking.
Malaysia's Home Ministry also declined to comment on the UN rescue appeal.
The issue would be discussed at a meeting of 15 countries, to be held in Bangkok on May 29, Thai junta spokesman Werachon said.
But the Royal Thai Navy said on Wednesday that its policy was not to send the boats back to sea.
"If they come to Thai waters we must help them and provide food and water," Rear Admiral Kan Deeubol told Reuters. "For human rights reasons, we will not send them back to sea."
Earlier this week, a junta spokesman said that a surge in migrants to Indonesia and Malaysia from Bangladesh and Myanmar had been caused by the crackdown and by Thai authorities blocking boats from landing.
Thailand ordered a clean-up of suspected traffickers' camps last week after 33 bodies, believed to be of migrants from Myanmar and Bangladesh, were found in shallow graves near the Malaysian border.
That has made traffickers wary of landing in Thailand, the preferred destination for the region's people smuggling networks, leading to many migrants being left out at sea.
'It's a policy matter'
A senior Malaysian maritime official said on Tuesday, after more than 1,000 people arrived on the Malaysian island of Langkawi at the weekend, that any more boats trying to land would be turned back
"We don't allow them in," said First Admiral Tan Kok Kwee, northern region head of the Malaysian Maritime Enforcement Agency. "It's a policy matter."
Indonesia provided food, water and medical supplies to around 500 passengers on a boat off the coast of the northwestern province of Aceh on Monday, before sending the vessel towards Malaysia.
The Indonesian Navy said the passengers of the boat they sent onwards wanted to go to Malaysia, not Indonesia.
A day earlier and also in Aceh, Indonesia rescued nearly 600 migrants from overcrowded wooden boats. Those migrants were brought ashore and remain on Aceh.
The Indonesian policy was to offer food and shelter to refugees and coordinate with international migrant and refugee bodies, Foreign Ministry spokesman Armanatha Nasir told reporters on Wednesday. This it had done with the nearly 600 migrants it rescued on Sunday, he added.
"What we do not do is load them on to the ship and push it to the ocean," he said.
But advocacy group ASEAN Parliamentarians for Human Rights criticised the Indonesian government for sending the boat back to sea on Monday.
"Towing migrants out to sea and declaring that they aren't your problem any more is not a solution to the wider regional crisis," ABHR Chairperson and Malaysian lawmaker Charles Santiago said in a statement.
Many of the arrivals are Rohingya, a stateless Muslim minority from Myanmar described by the United Nations as one of the most persecuted minorities in the world.
'Blood on their hands'
An estimated 25,000 Bangladeshis and Rohingya boarded rickety smugglers' boats in the first three months of this year, twice as many in the same period of 2014, the UNHCR has said.
"When countries such as Thailand implement a push back policy, we find Rohingya bodies washing ashore," said Sunai Phasuk at Human Rights Watch in Thailand.
"If these three countries move forward with push backs, blood will be on their hands."
Malaysia's police chief said that joint work with the Thai police force had helped Malaysian police smash seven syndicates involved in smuggling and trafficking in March and April.
The syndicates operated in northern Malaysia and southern Thailand, Khalid Abu Bakar told reporters on the Thai island of Phuket, where members of the two police forces met this week for annual talks on international crime.
Among 38 people arrested were two Malaysian policemen, he said.
As well as trafficking, Malaysian police believe the syndicates were involved in forging UNHCR documents, he said.
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