The public safety department in north-central Para state said 19 people were confirmed dead so far after a boat sank on the Xingu river late Tuesday.
That vessel, the Capitan Ribeiro, had 49 people on board, of whom 23 were rescued and seven remained missing, the department said in a statement.
Separately, the navy said 22 people died when a ferry sank early Thursday off the northeastern state of Bahia.
That boat had 133 people on board, of which at least 21 had been rescued, naval commander Flavio Almeida told AFP.
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There was no immediate information about the causes of the two sinkings.
Newspaper Folha de Sao Paulo said the boat in Para, in a northern Amazon region, may have been caught in a storm.
The vessel in the fatal incident in Para had left the port of Santarem bound for Vitoria de Xingu.
Ferries, fishing vessels and big commercial ships ply the Amazon waterways as one of the main forms of transport in a region with relatively few roads.