The gruesome discovery of the sites thought to contain dozens or possibly hundreds of remains of migrants from Myanmar and Bangladesh, follows a similar find this month across the border in Thailand.
Prime Minister Najib Razak made the announcement via Twitter, a day after Indonesia joined Kuala Lumpur in agreeing to take in the refugees, most of whom have fled Myanmar.
The "boat people," as they've been called, have been stranded at sea for weeks with little food or water. Indonesia and Malaysia say they will take them in temporarily.
At least 1,000 are still stranded offshore in rickety boats with little food or water. But so far, the governments of Southeast Asia have shown no willingness to let them come ashore.
Malaysia and Indonesia have also turned away the Rohingya, who have fled persecution in Myanmar. The migrants also include Bangladeshis who are escaping poverty in their country.
The Muslim minority has long been persecuted in the country also known as Burma. Many Bangladeshis were also rescued.