Eighty-two people have been rescued so far in an ongoing search off western Malaysia after the boats sank in separate incidents early Wednesday.
The boats, both believed to be bound for the neighbouring Indonesian island of Sumatra, were carrying illegal migrant workers heading home for the Muslim fasting month of Ramadan.
Adnan Abdullah, head of criminal investigations in central Selangor state, said police had detained two Indonesians believed to be the shipping agent and coordinator of the boat that sank off Port Klang with 97 people aboard.
The Star daily reported the men, aged 44 and 54, were arrested early Friday at a premise in Port Klang, the country's main port. Both have valid travel documents.
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Twelve men and three women have died, while 27 others remain missing.
The second vessel carried 27 passengers and sank slightly south near the district of Sepang. Twenty from that boat have been rescued, while seven are missing.
"The weather is clear. But we have not found anybody today," Zuhri Mat Akhir, a spokesman with the Malaysian Maritime Enforcement Agency, told AFP.
Officials believe some of those yet to be accounted for have made it to land nearby and fled to avoid being apprehended by authorities.
Investigations are underway but officials said both boats sank in rough seas and were overloaded - with the first one carrying more than three times its capacity.
Large numbers of Indonesians - many of them illegal migrants - return home annually from Malaysia for Ramadan, which begins next week and ends in late July, culminating in Eid al-Fitr, Islam's biggest festival.
Around two million illegal immigrants are estimated to be working in Malaysia, filling mostly low-paying jobs on plantations, construction sites, factories and other places.
Indonesians make up the bulk, while the rest are mostly from other poorer regional countries, such as Bangladesh and Myanmar.