Some survivors reportedly swam to shore while others were rescued by other boats in the area but the authorities do not know how many survived.
Brazil's navy joined dozens of rescue workers, including 15 divers, to search the area.
Rescue workers recovered the bodies of at least 15 people before the search was called off for the night, Brazil's official news agency Agencia Brasil said.
Da Silva said most of those who died were women and several dozen people remained unaccounted for.
The authorities said bad weather and overloading of passengers and cargo could have caused the ferry, which was grounded early this year, to sink.
The navy issued a statement saying the boat had been declared unfit for use after failing an inspection in January because it lacked the proper paperwork and a qualified crew, according to Agencia Brasil.
Al Jazeera's Gabriel Elizondo said from Brazil that boats on the river were usually flimsy.
The search is scheduled to resume on Monday, and an investigation into the cause of the accident is expected to take at least three months.