An estimated 18 people had been rescued and one passenger was confirmed dead after the ferry sank on Monday.
About 130 people have been reported missing by relatives in the area but it was not clear if they were all on the vessel, authorities said.
Authorities have deployed rescue vessels to the scene but bad weather has halted the operation for the night.
Indonesian rescue workers fought heavy rains and two-metre waves on Tuesday in a search for survivors after a ferry with at least 140 passengers on board sank in Lake Toba, a popular tourist destination in North Sumatra.
As you know, the boat capsized on lake Toba in North Sumatra on Monday evening, June 18.
The police statement said that on Tuesday morning the search had found several bags including one containing a mobile phone and ID, jackets and other items of clothing as well as traces of oil and a blue bucket and jerry cans suspected to be from the sunken ferry KM Sinar Bangun.
"It might take time to find victims who drowned", he added.
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The wooden ferry had a capacity of 60 passengers but was overloaded and also carrying dozens of motorcycles, said Sri Hardianto, an official at Indonesia's transport ministry.
"There are 65 people who say their relatives are missing".
At least 128 people are missing after a ferry sank in Indonesia, an official has said.
Disaster agency spokesman Sutopo Purwo Nugroho said the boat sank at about 5:30 p.m. Monday as it sailed from the mainland to an island.
Lake Toba, a popular tourist destination promoted by the government, fills the caldera of a giant dormant volcano and is the largest lake in Indonesia and one of the deepest in the world.
So far, rescuers have rescued 19 passengers of the boat, said Riadil Lubis, head of the provincial disaster management agency.
Ferry tragedies are common in Indonesia, an archipelago of more than 17,000 islands, with weak enforcement of safety regulations often to blame.