Malaysian police teams have begun sifting through a series of camps in the jungle.
Authorities believe that many of the migrants had been held for ransom by gangs of human traffickers.
They have dug up 139 graves but the number of bodies exhumed has not been made public.
Malaysian police say they have found signs of torture.
Some migrants were apparently held in "human cages" made of wood and barbed wire.
Malaysian Home Minister Ahmad Zahid Hamidi says many of the victims may have been killed after families failed to pay exorbitant ransoms to the traffickers.
"Today the chief and deputy chief of police are near the Thai-Malaysia border to identify and verify the mass graves that were found by police special forces and the civil defense force. These graves are believed to be related to human trafficking activities involving migrants."
International aid organizations say some migrants had been held captive for several months in these jungle camps.
Jeffrey Labovitz, Chief of Mission for the International Organization for Migration (IOM) in Thailand says migrants had been deprived of food, resulting in starvation.
"We have helped about 60 individuals with Beriberi in Thailand. We know of other 60 to 100 in Malaysia, so where are the rest? There's hundreds who did not make it. They could not walk. Some of them, we know made it to Malaysia in wheelbarrows, some of them made it on the backs of their friends. But a lot of them, perhaps hundreds, which is what we're finding, are buried in the forest between Thailand and Malaysia."
The discovery of the camps in Malaysia comes after similar graves were uncovered 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.
Thailand has also launched a "floating naval base" to help migrants stranded at sea.
But Thai Prime Minister Prayuth Chan-ocha says only those needing serious medical treatment will be taken ashore.
"We are setting up a center and joint task force to search and assist migrants found at sea. It's not that we don't value human lives. We have used measurements regarding Rohingya that their lives and safety comes first. We have boat patrols, but we have not found any migrants boats. We have navy aircraft patrolling in the sky and we haven't found any migrants either."
Authorities in Myanmar have started cracking down on the vast human trafficking network in the country. Earlier this week they nabbed 20 traffickers on board a rickety vessel crammed with over 200 migrants.
But the law has been too slow at crushing this lucrative trade, as thousands choose to flee poverty or persecution at home, in search of greener pastures.
For CRI I'm Poornima Weerasekara.
