There were 21 people reported safe among the estimated 60 aboard the boat, which capsized off southern Johor state around 4.30am (3.30am in Thailand), Reuters reported.
The survivors and the boat were found on a beach in Tanjung Balau and the Malaysian Maritime Enforcement Agency said a search and rescue operations had been launched for those missing.
Authorities did not provide further details about the origin or nationality of the migrants, or their intended destination.