"Based on the size of the graves, and after the area was cleared... We have a clearer indication -- single grave, single person," Deputy Home Affairs Minister Wan Junaidi Tuanku Jaafar told reporters.
When asked by AFP if he believed that there are 139 bodies since Malaysia has previously said it had discovered 139 grave sites, Wan Junaidi said: "Yes".
The minister said initial investigations showed the bodies were wrapped in white cloth, in accordance with Muslim tradition, and were marked with wooden sticks.
Malaysian police said earlier this week that a total of 139 grave sites and 28 recently abandoned camps had been found along the northern border with Thailand, capable of housing hundreds of people.
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Malaysian police believe they were used by human-traffickers and smugglers. Thai police in early May had uncovered similar camps on their side of the border.
That left boats loaded with hundreds of starving migrants stuck at sea. Malaysia and Indonesia recently agreed to let vessels land safely following an international outcry.
Malaysian police said 37 people have been arrested this year on suspicion of human-trafficking, but have given no details.
In Thursday's press conference, Wan Junaidi said Malaysian security forces had not been patrolling the area where the grave sites were found because they were seen as being inaccessible.
Malaysian police commandos surveyed the area starting from May 11 after the discovery of the graves in Thailand, he said.