"We cannot welcome them here," Malaysian Deputy Home Minister Wan Junaidi Jaafar told CNN by phone.
"If we continue to welcome them, then hundreds of thousands will come from Myanmar and Bangladesh."
The comments come as humanitarian groups issue urgent warnings about the fates of estimated thousands of desperate migrants stranded aboard rickety traffickers' ships in the busy Strait of Malacca and nearby waters, looking for a safe harbor to take them in.
Jeff Labovitz, spokesman for the International Organization Migration in Bangkok, told CNN Thursday that Thai authorities were dealing with one such vessel with 350 passengers on board -- including "many women and children" -- after it had been abandoned by the trafficker operating the vessel.
"We don't know if they're going to let it disembark," he said.
He said those on board had earlier been given food and water by Malaysian authorities, before being turned around.
The humanitarian crisis engulfing Myanmar's Rohingya -- a persecuted Muslim minority who are effectively stateless in majority-Buddhist Myanmar -- has begun impacting other southeast Asian countries as desperate migrants arrive in their waters and on their shores, seeking asylum.
More than 1600 migrants -- both Rohingya and economic migrants from Bangladesh -- have landed in Malaysia and Indonesia since Sunday, officials say, after Thai officials began cracking down on human trafficking camps operating in the country's south near the Malaysian border, disrupting established people smuggling networks.
The crackdown came following the discovery of dozens of bodies in trafficking camps in the jungle.
With the Thai pipeline for illegal migrants closed, overcrowded traffickers' boats have begun offloading their human cargo on the shores of Malaysia and Indonesia -- Muslim-majority countries that have shown sympathy for the Rohingya in the past.
Alternatively, crews have simply abandoned them to drift.
Rights groups have called on governments in the region to carry out urgent search and rescue operations to avoid a catastrophe for thousands stranded at sea.
"It's harrowing to think that hundreds of people are right now drifting in a boat perilously close to dying, without food or water, and without even knowing where they are," said Kate Schuetze, Asia Pacific researcher for rights group Amnesty International.
'Send them back'
But despite the calls to rescue the imperiled migrants, officials from Malaysia and Indonesia have said they have instead refueled and restocked migrant vessels and sent them on their way.
"If the boat is still good and can sail back, we give them food, and drink and fuel and send them back," the Malaysian minister said.
He denied reports that Malaysian authorities had "pushed back" a boat with more than 500 migrants off the coast of northern Penang Wednesday after providing them with fuel and supplies -- but said that doing so would be consistent with government policy, provided the vessel was seaworthy.
Arrmanatha Nasir, a spokesman for the Indonesia's Foreign Ministry, told reporters Wednesday that an Indonesian ship had given provisions to a migrant boat it encountered on patrol in the Strait of Malacca before the boat carried on its way to Malaysia -- which he said was its intended destination.
"The people on the boat did not want to go Indonesia, but they asked for help, clean water and food," he said. "After the aid was given, they parted."
Indonesia was currently providing food and shelter to 582 migrants rescued from boats off the coast of Aceh Sunday, and was working with international bodies to provide them documentation and temporary relocation, he said.
'Diseases, social problems'
Malaysia is processing more than 1,000 recently arrived migrants, with the aim of sending them home, said Wan Junaidi Jaafar.
He said the 1,058 new arrivals on Langkawi Island had been transferred to another state, and were in the process of being repatriated.
"The policy is to send them back," he said.
"They come with the culture and come with diseases and lots of social problems. Do you realize Malaysia has been free of TB and many kinds of diseases, and these people are bringing many of this together?"
He said that some of the migrant boats had been deliberately capsized, and that "the sentiment of the people is completely against immigrants."
Malaysian state media Bernama reported Wednesday that residents of Langkawi were expressing concerns about security following the mass arrivals, and quoted some as saying they believed there were migrants still hiding in the jungle.
"We have seen bite marks on the fruits of the trees that we have planted, and even heard children crying at night in the jungle," one man said.
In a statement Thursday, Human Rights Watch urgently called on Malaysia, Indonesia and Thailand to end their "pushbacks" of migrant boats and "instead bring them ashore and provide desperately needed aid."
"The Burmese government has created this crisis with their continued persecution of the Rohingya," said Phil Robertson, deputy Asia director at Human Rights Watch.
"Thailand, Malaysia, and Indonesia have made things much worse with cold-hearted policies to push back this new wave of 'boat people' that puts thousands of lives at risk."
Rohingya have been fleeing Myanmar, also know as Burma, in the tens of thousands, in the wake of an outbreak of communal violence in 2012 and what's been described as the ethnic cleansing of the minority.
Myanmar, a majority Buddhist country, considers the Rohingya to be interlopers from neighboring Bangladesh, despite the fact that many have lived there for generations.
Denied citizenship, they live under apartheid-like conditions
, with 140,000 in Rakhine State forced to live into crowded camps which they are generally forbidden to leave.
As a result, many have been attempting to leave by sea. A report by UNHCR
, the U.N.'s refugee agency, said that about 25,000 people had fled Rakhine State and Bangladesh by sea in the first quarter of 2015, with an estimated 300 dying in the process.
In an interview with Radio Free Asia
Wednesday, a senior official from Rakhine State denied that the hundreds of migrants who had come ashore in Malaysia and Indonesia hailed from his region.
Maung Maung Ohn, the chief minister of Rakhine State, said it was "impossible" that the rescued migrants were from Rakhine.
"Rakhine State is stable right now," he said.
"Is it impossible that the boat people in Malaysia and Indonesia are from Myanmar. It was possible in the past, but now it is ... almost impossible."