The fibreglass boat overturned and sank late yesterday with around 70 people onboard as a patrol vessel was pursuing it off the state of Johor, said Aminuddin Abdul Rashid, an official with the Malaysian Maritime Enforcement Agency.
Those aboard wanted to sneak out of Malaysia to return to their homes in Indonesia to celebrate the end of the Muslim fasting month of Ramadan, he said.
Boat accidents are common in Malaysia which draws hundreds of thousands of illegal immigrants from poorer regional countries who fill factory, plantation, construction and other mostly low-paid jobs shunned by locals.
Aminuddin said 59 passengers had been rescued in addition to the two boatmen who were also pulled from the water today, clinging onto some wood.
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According to the boatmen, the vessel was carrying 70 people, he said, adding that a man and a woman had died.
"So nine are still missing," Aminuddin told AFP.
Another agency official had earlier said the boat was believed to be carrying around 80 people with 18 missing.
The collision caused damage to the passenger vessel and it sank three nautical miles off Tanjung Piai, peninsular Malaysia's southern-most point, in strong currents.
Aminuddin said the two boatmen were being investigated for smuggling the migrants and could face jail if charged and found guilty.
"It's not easy to educate them," he said, referring to the migrants who are believed to have paid 1,500 ringgit (USD 470) each for the dangerous journey back to avoid border controls.