The discovery could be a major breakthrough in the search for the vessel which sank last Monday on Lake Toba, a picturesque tourist destination in Sumatra.
An object measuring 20 metres by five metres was found at a depth of 450 metres (1,475 feet) on Sunday, said Muhammad Syaugi, head of the national search and rescue agency.
"The shape of the silhouette is like that of a ship," Syaugi told AFP.
However, further analysis would be required to confirm if it was the stricken vessel, he added.
Lake Toba, which fills the crater of a supervolcano that exploded in a massive eruption tens of thousands of years ago, is one of the world's deepest lakes, plunging some 500 metres in spots.
Due to its depth, search teams will use remotely operated underwater vehicles to help identify the object.
Three passengers have been confirmed dead in the accident, with 18 survivors. Official estimates listed 193 others -- including children -- as missing.
The traditional wooden boat could have been carrying five times the number of passengers it was built to hold, along with dozens of motorcycles, officials have said.
The vessel is believed to have been operating illegally with no manifest or passenger tickets and authorities have struggled to pinpoint the exact number onboard when it went down in bad weather.
The missing toll has raised fears that many bodies are trapped inside the ferry at the bottom of the lake.
The accident could be one of Indonesia's deadliest maritime disasters.
National police chief Tito Karnavian said investigators had uncovered a range of violations.
Four suspects have been named, including the boat captain, as well as three senior officials at Simanindo port, he said.
"These three people were supposed to monitor and check (vessels') seaworthiness," Karnavian said.
Survivors have said the boat began shaking as it struggled to navigate strong winds and high waves about halfway into the 40-minute trip from an island in the middle of the lake to shore.
Traditional vessels like the one in the Lake Toba disaster are often packed beyond capacity and lacking safety equipment.
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