Ahmad Zahid said the camps identified are in the areas of Klian Intan and villages near the border.
A mass grave was discovered in Thailand’s southern Songkhla province earlier this month
“They have been there for quite some time. I suspect the camps have been operating for at least five years,” he said.
A police spokeswoman declined to comment, saying a news conference on the issue would be held on Monday.
A police official who declined to be identified said police commandos and forensic experts from the capital, Kuala Lumpur, were at the site but it was unclear how many graves and bodies had been found.
“Of course I believe that there are Malaysians involved,” Ahmad Zahid said, when asked about possible involvement of locals in the incident.
Thousands of migrants – Rohingyas fleeing persecution in Myanmar and economic migrants from Bangladesh – are stranded in boats in the area.
Watch John Sparks’ report from May 16:
More than 3,000 have landed in neighbouring Malaysia, Thailand and Indonesia.
Malaysia and Indonesia have begun searching for migrant boats in the past week. Myanmar also rescued the first boat two days ago.
Indonesia and Malaysia agreed to end their policy of pushing migrants boats back out to sea on Wednesday, and instead said they will provide temporary shelter to thousands stranded at sea.
Watch our report on the Muslim minority from August 2013.