Malaysian Prime Minister Najib Razak has said the country's navy will conduct search and rescue missions for Rohingya boats in the Andaman Sea.
Humanitarian aid would also be delivered by land and sea, he said.
His announcement comes after weeks of authorities rejecting migrant boats and towing them out of Malaysian waters.
Malaysia and Indonesia's foreign ministers are in Myanmar for talks on the migrant crisis. About 7,000 people are believed to be still out at sea.
The migrants are comprised of Rohingya Muslims fleeing persecution in Myanmar as well as Bangladeshis.
Malaysia and Indonesia have said they will temporarily shelter those that land on their territory but need help from the international community.
'Ping-pong'
Mr Najib said on his Twitter account that it was "basic human compassion" to provide aid to the hungry and sick.
Malaysia was among several in the region that had refused to take in the migrants and had been towing the boats to other countries' waters, in what observers have condemned as a deadly "ping-pong" match.
Meanwhile Malaysia Foreign Minister Anifah Aman's office said he would hold talks Thursday with his Myanmar counterpart U Wunna Maung Lwin in the capital, Nay Pyi Taw.
Myanmar has been accused of doing nothing to address the problem at home.
It did not send a representative to a meeting of regional foreign ministers on Wednesday where the deal to provide temporary shelter and not turn back boats was reached.
Amnesty International's Asia Pacific Director Richard Bennett said Wednesday's decision to provide shelter helped those who have come ashore, but "does nothing for the thousands still adrift at sea, with diminishing supplies of food and water, or for any more who may follow them."
Thailand has said it will stop towing boats back to sea, something Malaysian and Indonesian navies have also been doing in recent days, but did not sign the agreement to provide shelter, saying it is already struggling to cope with tens of thousands of refugees from Myanmar.
More than 3,000 have been rescued by locals or come ashore in Indonesia and Malaysia.
Malaysia and Indonesia have appealed for help from other nations to resettle the migrants within a year.
The US State Department said the US was prepared to take in refugees and lead a multi-country effort to resettle them.
Myanmar (also known as Burma) sees the Rohingya as migrants from Bangladesh, though many generations have lived there. It restricts their movements and personal lives, and Rohingya have faced persecution from the majority Buddhist population.
The BBC's Jonah Fisher, who is in Sittwe province where many of the migrants are believed to have come from, says unless the root cause is addressed the migration problem will continue.