The trio were among just 18 people rescued after the vessel capsized and sank on Monday (June 18) at Lake Toba, a picturesque tourist destination in Sumatra.
Three passengers have been confirmed dead, but official estimates listed 193 others – including children – as missing.
That has raised fears the sinking could be one of Indonesia’s deadliest maritime disasters.
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.
Captain Tua Sagala and two of his crew would be questioned, said local police chief Marudut Liberty Pandjaitan.
Sagala is also the boat’s owner, he said, adding that a fourth crew member who survived the accident had since fled the area.
“(He) is still at large,” Pandjaitan told reporters.
Earlier yesterday, national police spokesman Yusri Yunus said the captain had not yet been questioned because he was “still traumatised”.
Meanwhile, hundreds of grief-stricken people prayed and sang hymns at the shore, hoping for news about missing loved ones.
Indonesia is a Muslim-majority country but the area has a large Christian population.
Some mourners expressed anger at the pace of the search effort.
Jadianto Nainggolan, 40, said a dozen relatives were on the boat including his three-year-old nephew.
He showed a picture of the group that he said was taken shortly before they got on the ferry, which has not yet been located.
“We’re hoping that our relatives will be found – we’re counting on the search and rescue agency,” he said.
“But I don’t think they’re doing enough – there seem to be more teams at the harbour than on the lake.
“There must be a lot of people trapped in the boat.”
The vessel is believed to have been operating illegally with no manifest or passenger tickets so officials have struggled to pinpoint the exact number onboard when it went down in bad weather.
They have relied on reports from survivors and the families of missing relatives who may have been on the doomed vessel.
The search-and-rescue operation is focused on recovering bodies – including those that may still be inside the sunken vessel.
It was not clear if any foreigners were on board.
Divers and underwater vehicles, along with about 400 personnel, are being deployed to search the enormous body of water.
Toba is one of the world’s deepest lakes, plunging some 500 metres in parts, and it covers an area of about 1,145 square kilometres.
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.
Lake Toba fills the crater of a supervolcano that exploded in a massive eruption tens of thousands of years ago.
Millions were travelling around Indonesia to celebrate the end of the holy month of Ramadan when the accident happened.
It came days after more than a dozen people were killed in another ferry accident in the Southeast Asian archipelago nation, where many people depend on boats despite the industry’s woeful safety record.
Traditional vessels – like the one in the Lake Toba disaster – are often packed beyond capacity and lacking safety equipment.
Nearly 80 people died in a ferry accident on Lake Toba in 1997.
More than 300 people are estimated to have drowned in 2009 when a ferry sank between Sulawesi and Borneo.