About 90 people were on the vessel that capsized off the island of Batam about 5 am, the island's police chief Sambudi Gusdian said.
A search effort underway for hours has rescued 39 people so far.
Haryanto, a 51-year-old survivor, said the speedboat capsized amid heavy rains and high waves about two hours after it left Johor Bahru in Malaysia.
He said the boat was overcrowded with standing room only. A police helicopter and more than a dozen boats are involved in the search and rescue effort.
Sinkings are common due to poorly enforced safety regulations.
One of the worst ferry sinkings in recent years occurred off Sulawesi in 2009, killing more than 330 people.