Malaysian police say 139 suspected migrant grave sites have been found in 28 people-trafficking camps along the Thai border.
National police chief Khalid Abu Bakar said some of the graves, found since 11 May, may contain more than one body.
They are close to an area of Thailand where trafficking camps and dozens of shallow graves were found this month.
The operation forced traffickers to move the migrants by sea instead. But thousands were left stranded after the traffickers abandoned them and no country would take them in.
The traffickers have been using the jungles of southern Thailand and northern Malaysia for years to smuggle people into Malaysia. Most of the migrants are Rohingya Muslims fleeing persecution in Myanmar, rights groups say, but others are Bangladeshis seeking employment in Malaysia.
“[In] the operation which we have been conducting from 11 May to 23 May we discovered 139 of what we believe are graves,” Khalid told reporters on Monday.
The camps were found along a 50-km (30-mile) stretch of the Thai-Malaysian border and were only hundreds of metres from the graves discovered in Thailand, he said.
Khalid was speaking at a press conference a day after the government first announced the discovery of Malaysian graves. He said the biggest of the camps could have held up to 300 people.
Officials are now exhuming the bodies to determine whether they were victims of human trafficking.
The International Organization for Migration (IOM) says since the Thai crackdown, they have found several people roaming in the Thai forests.
Jeffrey Labovitz, chief of mission in Thailand for the IOM, said they had screened people rescued from detention or shelters in Thailand and found some inflicted with beriberi – a diseases caused by a vitamin B1 deficiency.
“It’s people who are skeletal, they have no fat on their body they’re just bones. They can no longer support their weight,” he told the BBC.
“They are no longer a commodity to smugglers they’re an example to others that they have to pay.”
Earlier, Malaysia Prime Minister Najib Razak said he was “deeply concerned with graves found on Malaysian soil, purportedly connected to people-smuggling”. Writing on his Facebook and Twitter accounts, he promised to “find those responsible”.