Natural Resources and Environment Minister Wan Junaidi Tuanku Jaafar said the four Indian nationals had been detained to assist in investigations.
The seizure by the Wildlife Crime Unit was worth an estimated RM600,000 (99 lakh rupees).
Wan Junaidi said two suspects were detained in the first raid at a house in the suburb of Petaling Jaya yesterday.
"A total of 1,011 Star tortoises and 23 Indian Roofed turtles were seized," the minister said.
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Wan Junaidi said the enforcement officers found 36 Black Pond turtles in four bags.
Checks showed all the four suspects did not possess any licence from the Wildlife and National Parks Department (Perhilitan) to keep the reptiles.
The suspects will be investigated under Section 68 of Malaysia's Wildlife Protection Act 2010 for keeping wildlife without a special permit.
The offence carries a jail term of up to three years, a maximum fine of RM100,000, or both upon conviction.