The boat sank after being hit by strong waves around midnight on Thursday, about 13.55 nautical miles off Tanjung Siang in Kota Tinggi of Johor state, located in the south of Peninsular Malaysia.
But the incident came to light only last evening when a group of fishermen rescued three of the survivors clinging to a plastic drum. A fourth survivor was rescued by a Malaysian Maritime Enforcement Agency (MMEA) patrol boat passing through the area.
Kota Tinggi police chief Supt. Mohd Nor Rasid said search and rescue operations by the Marine Operations Force and MMEA are still ongoing.
Shipping accidents off Malaysia's coast are common as thousands of people from poorer neighbours, such as Indonesia and Myanmar, risk journeys in flimsy boats to work illegally in the relatively affluent country.
It was the second recent maritime accident involving Indonesians in Johor state's waters. At least one woman drowned and 27 were rescued when a boat sank July 18.