The deadly accident comes the same day as authorities officially called off the search for some 164 people still missing after another ferry sank on a popular tourist lake two weeks ago.
Images from the latest accident showed passengers clinging to the side of the KM Lestari as it tipped in waters off Sulawesi island, while other passengers floated in the sea awaiting help.
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The ferry began taking on water from a leak in its hull, Indonesia's transportation agency said, as waves swamped trucks and other vehicles on the boat's deck before they plunged into the water.
At least six people have died, but authorities have not yet accounted for all 139 people listed in the ship's manifest, local police spokesperson Dicky Sondani told Kompas TV.
The transportation agency said passengers had been wearing life jackets.
"Some passengers have been successfully evacuated," it added in a statement.
The vessel was sailing from Sulawesi to nearby Selayar island when it ran into strong winds and high waves.
Maritime accidents are common in Indonesia, where many people depend on boats to get around the 17,000 island archipelago nation.
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