Hopes are fading for 44 people still missing more than a day after an overcrowded speedboat carrying Indonesian migrant workers capsized and sunk in rough seas, claiming at least 18 lives.

The search resumed at first light Thursday around Batam, an Indonesian island south of Singapore, with roughly 125 personnel combing the seas for any sign of survivors, local disaster agency section chief Hardin Nafii told AFP.

"We pray that hopefully those still missing are saved, and are alive," he said.

The speedboat was carrying 98 passengers and three crew from Malaysia to Batam early Wednesday morning when it ran aground on a reef in bad weather and capsized, the disaster agency said.

Rescue teams pulled 18 bodies and 39 survivors from the sea, but called off the search as light faded. Forty-four others remain unaccounted for more than a day after the accident.

Police said the passengers were likely illegal Indonesian migrant workers returning from jobs in Malaysia, and the boat was over capacity at the time of the accident.

The disaster agency revised up the passenger numbers late Wednesday from 93, saying the lack of a manifest made it difficult to establish exact figures aboard.

The Indonesian archipelago of more than 17,000 islands is heavily dependent on boat transport, but safety standards are lax and fatal accidents common.

More than 60 people died in December when huge waves capsized a ferry charting a course through Sulawesi province.