The Virgo Transport 8 ship carrying 243 people went missing in bad weather early on Sunday, the rescue agency said.
Authorities have rescued 108 people from the ship, which was travelling from Surabaya in East Java to Banjarmasin in South Kalimantan.
"We have continued the search for the missing since early in the morning. We are deploying 622 personnel and around 12 ships," I Putu Sudayana, head of the Banjarmasin rescue agency, told Reuters.
There was no increase in the death toll of six as of Monday morning.
In a video shared by the rescue agency, a large red-and-black ship lies capsized and partially submerged in choppy blue water, with its red-painted underside visible above the surface.
Two small boats, each carrying people, were seen floating near the capsized ship in rough water.
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, 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.
with AP
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