Sahrul Arifin, the head of emergency and logistics at the East Java Disaster Mitigation Center said there were about 76 people rescued so far from the sea disaster.
Bad weather caused by a tropical depression south of the Philippines which claimed more than 200 people, may have caused the incident. There were also reports of overloading which may have contributed to the sinking of the boat Saturday night.
"Our search and rescue team have begun sweeping the water around where the accident took place but we are now sending body bags to that area," Arifin said.
One of the survivors, Esmat Adine said the ship started rocking from side to side, triggering widespread panic.
Because people were so tightly packed, they had no where to go, said the 24-year-old Afghan migrant.
"That made the boat even more unstable and eventually it sank," he said in a report by smh.com.au
Passengers of the wooden boat were believed to be coming from the Middle East and Asian countries, including Iran, Iraq, Afghanistan and Pakistan.
Many of the migrants coming from these countries use Indonesia a transit point en route to Australia to seek asylum.
Australia has become a popular destination for asylum-seekers from Afghanistan and Sri Lanka and some Middle East countries. At one point, there were around 6,000 of them waiting for their applications to be processed.
Media reports say many of them pay thousands of dollars to board boats that are not seaworthy or poorly equipped. There were reports these boats are operated by Indonesian-based groups in their people-smuggling activities.
Many of the refugees have been languishing for many years in prison-like facilities
on Christmas Island off the Australian coast and other detention centers in mainland Australia.