The mass graves were found near 17 abandoned camps in Padang Besar area on the Thai side of the border and they are believed to be a part of human-trafficking activities involving migrants, Home Minister Zahid Hamidi said.
The Minister said the General Operations Force (GOF) had found 14 large tents and three other smaller tents, believed to have been operational for at least five years but were abandoned when the authorities came to the location.
As governments in Thailand, Malaysia and Indonesia have launched crackdowns amid intensified international spotlight, human traffickers have abandoned camps on land and even boats at sea to avoid arrest.
In many instances, these traffickers have been paid by the miniority Rohingya Muslims from Myanmar to help them flee to Malaysia or Indonesia.
A few weeks ago hundreds of Muslim Rohingyas were found crammed in boats heading to Malaysia and Indonesia.
Human rights groups and activists say the area on the Thai-Malaysia border has been used for years to smuggle migrants and refugees, including Rohingya Muslims, a persecuted minority in Myanmar.
Since May 10 alone, more than 3,600 people - about half of them from Bangladesh and half Rohingyas from Myanmar - have landed ashore in Indonesia, Malaysia and Thailand.
Mass graves were discovered in Thailand earlier this month mostly in southern Songkla province bordering Malaysia.
The Rohingya, numbering around 1.3 million in Myanmar, are believed to be one of the most persecuted minorities in the world.
