On Sunday, Edy Prakoso, another official at the national rescue agency, said the ship leaned heavily to one side after strong waves hit its starboard side.
A passing helicopter reported the vessel had capsized, Transport Minister Dudy Purwagandhi said on Sunday, with the cause still being investigated.
Indonesia relies on ferries across its 17,000 islands, where sea travel is cheaper and more accessible than flying, and there have been numerous accidents.
In separate incidents last month, two ferries carrying hundreds of passengers caught fire in waters. Five people died when a ferry caught fire off Madura island, while one person died in a fire on a ferry travelling from the tourist island of Bali.
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