Initial reports say the capsized vessel carrying at least 60 migrants sank off the southern state of Johor and authorities have dispatched rescue boats and an aircraft to find those missing.
Ten bodies have been found and 29 people were missing after a boat carrying suspected illegal migrants capsized off Malaysia in bad weather.
There were 21 people reported safe among the estimated 60 aboard the boat, which capsized off southern Johor state around 4:30 a.m. (2030 GMT) on Wednesday.
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.
Soldiers on patrol discovered the bodies of seven men and four women on the shore, coastguard chief Admiral Mohamad Zubil Mat Som said
Another 20 men and two women were found alive following the voyage from a nearby Indonesian island, and have been taken into custody, he said.
Those missing are believed to have fled into hiding or drowned, and authorities have deployed boats and an aircraft to hunt for them.
"We deeply regret this deadly tragedy," Mohamad Zubil told AFP. "I urge migrants not to enter Malaysia illegally."
Relatively affluent Malaysia is home to millions of migrants from poorer parts of Asia, many of them undocumented, and they work in industries including construction and agriculture.
Indonesians looking for work sometimes try to enter neighbouring Malaysia illegally by making sea crossings in rickety boats, and accidents hap pen regularly.