"A wooden boat with 97 Indonesians has sank off Port Klang near Banting," Mohamad Zuhri, spokesman for the Malaysian Maritime Enforcement Agency, told AFP, adding that 31 had been rescued.
"The Indonesians were trying to enter Malaysia illegally by crossing the Malacca Strait."
He said the boat sank overnight, but had no details on what caused the accident or what the vessel's capacity was.
Authorities said one helicopter and five vessels had been deployed to search for survivors.
Relatively affluent Malaysia, Southeast Asia's third-largest economy, is a magnet for migrant workers from poorer neighbours such as Indonesia, Bangladesh, and Myanmar.
Accidents are frequent as thousands annually risk the sea journey in rickety boats to seek low-paying work, typically shunned by Malaysians, on plantations, construction sites and in factories.
Indonesians -- by far the most numerous of arriving illegals -- often chose to cross the narrow Malacca Strait under the cover of darkness.