Clovis Araujo, a Brazilian fire department spokesman, said 92 people had been rescued by small boats and the state's floating police station - a 10-metre vessel that travels along the river and was in the area at the time of the collision.
Rescue teams recovered the bodies of four children, four women and one man, he said.
Survivors were taken to the small nearby town of Novo Remanso and sheltered in the local church.
They were due to be flown out of the region by helicopter to Manaus, the state capital.
"We will keep searching until the last body is found," Araujo said.
Many of those missing were likely to be passengers who were asleep in cabins inside the two-story wooden vessel and were unable to get out before the boat sank, said Aguinaldo Rodrigues, a state public safety department spokesman.
"As far as we can tell, just about all the survivors were passengers sleeping in hammocks on the deck,'' Rodrigues said.
Rodrigues said it was too early to determine the cause of the accident, but said that visibility was "very poor" at the time of the collision.