A nine-year-old boy survived the crash, which happened after one of the engines failed, relatives of the four survivors said.
Pereira said that the pilot had told air traffic control that he wanted to return to the departure airport in Coari because of bad weather.
The aircraft hit the crown of a tree before plunging into the Manacapuru River, Roberto Rocha, undersecretary of civil defence, said.
Local media reported that those who survived the crash had opened the door and left the aircraft as it was sinking under the water.
About 40 firefighters, including nine divers, and civil defence officials searched throughout Saturday night for survivors.
Officials believe that the aircraft attempted an emergency landing at the nearby Panamacapuru airport but crashed in the river instead.
An investigation is under way.
The EMB-100 Bandeirante turboprop, made in Brazil, was said to have undergone all of its safety maintenance checks, and had up to date documentation, Brazil's Civil Aeronautics Agency said.