Six people have been confirmed dead and 108 rescued, National Search and Rescue Agency chief Mohammad Syafii said.
Five aircraft and 17 vessels, including navy warships, were deployed to search waters around the wreck.
"We will maximize the search operation in six sectors that we have divided by prioritizing the search for floating victims," Syafii said.
"Hopefully, we can find the victims in safe condition."
Divers and underwater drones will also search the wreck, which rescuers have located.
Transportation Minister Dudy Purwagandhi said the ferry was not overloaded and had a maximum capacity of 500 people.
Maritime accidents are common in Indonesia, an archipelago of more than 17,000 islands where boats are a major form of transportation. Poor safety standards and unpredictable weather have contributed to past disasters.