"Many people have reported their relatives missing," Budiawan, head of the search and rescue agency based in the nearby city of Medan said.
About 18 people reportedly have already been rescued, one passenger has been confirmed dead.
"It might take time to find victims who drowned," he said, adding that some bodies may be trapped inside the sunken vessel.
Indonesian rescue workers fought heavy rains and two-meter waves on Tuesday in a search for survivors after a ferry with at least 80 passengers on board sank in Lake Toba, a popular tourist destination in North Sumatra.
The National Disaster Mitigation Agency said there were unconfirmed reports of up to 130 people on board the ferry.
Lake Toba, a popular tourist destination, fills the crater of a giant dormant volcano and is one of the deepest lakes in the world.