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.