The boat capsized near the southern Malaysian state of Johor, an official from the Maritime Enforcement Agency said.
“The boat was overloaded, and the seas were rough so it sank,” he said, adding that search and rescue efforts for those still missing were under way.
He said the boat had been carrying around 50 passengers but the exact number was not known.
Authorities were alerted to the accident when a woman passenger made an emergency call on her mobile phone to a special safety hotline set up by the maritime agency, he said.
Agency and marine police personnel rushed to the scene to pull passengers, including two children, from the water.
Boating accidents along Malaysia’s coast are common as the relatively affluent country draws thousands of people from poorer regional neighbours such as Indonesia and Myanmar, usually seeking to work illegally.
Ten Indonesians, including two pregnant women, drowned in December when their boat capsized in rough seas also off Johor.
Also last month, nearly 500 people from Myanmar illegally entered Malaysia when they swam ashore at the end of a boat journey. One person died.
They were believed to be one of the largest groups of Rohingya Muslims to have reached Malaysia this year after fleeing sectarian violence in Myanmar.