Malaysia has begun exhuming bodies suspected to be migrantsburied in 139 grave sites close to the Thai border.
Authorities believe the migrants were held for ransom in jungle camps by gangs of human traffickers.
Thousands of migrants from Bangladesh and Myanmar have left for Thailand, Malaysia and Indonesia in recent weeks.
Thailand has offered a "floating naval base" to help migrants stranded at sea but said only those needing serious medical treatment will be taken ashore.
Meanwhile, authorities in Myanmar have charged 20 people with offences related to human trafficking. They were arrested from a vessel carrying 200 migrants from Bangladesh that was rescued last week.
'Shocking cruelty'On Tuesday, Malaysian police teams began sifting through a series of camps found in the jungle near the country's border with Thailand.
Some migrants were apparently held in "human cages" made of wood and barbed wire at the camps, which officials believe were only abandoned recently.
Malaysian national police chief Khalid Abu Bakar said there were signs that torture had been used, but he did not elaborate. "We were shocked by the cruelty," he told reporters.
The discovery of the camps in Malaysia followed the uncovering of similar graves on the Thai side of the border at the beginning of May.
After those graves were found, Thailand began cracking down on the routes used by traffickers to move Bangladeshi migrants and Rohingya Muslims from Myanmar through its territory.
The migrants, who want to reach Malaysia, were instead being sent by sea, but thousands were left drifting as no country wanted to take them in.
The UN's refugee agency says about 3,000 people have now reached land, but estimates another 2,600 may still be out at sea.
Last week, Malaysia and Indonesia agreed to stop rejecting boats and to provide temporary shelter to the migrants.
But while Thailand said it would stop towing boats away from its territory, it said it would not take in migrants.
Facing international pressure to do more, Thailand's Prime Minister Prayuth Chan-ocha said this week that the country would establish a "floating naval base" to help migrants.
But this seems like an attempt to keep the boats at arms' length rather than a display of genuine desire to help the migrants, according to the BBC's Jonathan Head in Bangkok.
A total of seven ships, two surveillance aircraft and two helicopters are involved in the Thai operation in the Andaman Sea - but only migrants with serious medical needs will be taken to land, where they will be considered illegal arrivals.
"If anyone is injured or sick, they can be treated at hospitals in Thailand but will face illegal entry charges - it is up to them to decide," he said.
Thailand has also agreed to allow US navy aircraft searching for migrants to operate from its bases after refusing a US request last week - but only if they do so under Thai military command.
Thailand is due to host a regional meeting on Friday to discuss the crisis.