The number of casualties was revised up on Saturday to 62.
Voepass said earlier that the ATR 72-500 was carrying 57 passengers and four crew between Cascavel in the southern state of Paraná to Guarulhos airport in São Paulo city. But it later confirmed there was another unaccounted-for passenger on the flight.
Footage circulating on social media showed a plane descending vertically, spiralling as it falls.
The aircraft crashed in a residential area, but no-one on the ground was injured. Officials said only one home in a local condominium complex was damaged.
Capt Maycon Cristo, a spokesman for the fire department which is helping with the recovery, said that so far, two people had been identified from evidence recovered at the scene.
He said that teams were relying on a number of factors to help identify passengers.
These include documents and the position of bodies in relation to seating, as well as mobile phones recovered from some of the victims.
Capt Cristo said the casualties were being moved to a police morgue in São Paulo.
Lt Ramatuel Silvino of the São Paulo civil defence service said family members would be staying in a hotel in the city.
The plane crash is Brazil's worst since 2007, when a TAM Express plane crashed and burst into flames at São Paulo's Congonhas airport, killing 199 people.
At this stage, it is not known what caused the ATR 72-500 to crash.
Authorities said the flight recorders had been retrieved.
ATR, the French-Italian plane maker, said it would co-operate with the investigation.
According to the tracking website Flightradar24, flight 2283 had taken off from Cascavel at 11:56 local time (14:56 GMT) on Friday and was due to arrive at 13:40.
The last signal received from the aircraft was about 20 minutes before it was scheduled to land.
Brazil's civil aviation agency said the plane, which was built in 2010, had been "in good operating condition, with valid registration and airworthiness certificates".
The four crew members on board at the time of the accident were all duly licensed and had valid qualifications, it added.
The Uopeccan Cancer Hospital in Cascavel told BBC Brasil that two of its trainee doctors were among the passengers who died.
The moment the passenger plane crashed was witnessed by local residents, while others described damage to their homes.
Luiz Augusto de Oliveira told Reuters that he, his wife and their maid were at home when "suddenly we saw the aircraft exploding in the backyard of my house".
He said: "At the time of the collision, we thought it was a helicopter breaking down, due to the noise."
He added that everyone in the house was unharmed and while there was some damage, it was "as minimal as possible, it was material goods. I just have to thank God for the way the aircraft crashed."
Another resident, Nathalie Cicari, told CNN Brasil she had been having lunch when she heard a "very loud noise very close by", describing it like the sound of a drone but "much louder".
"I went out on the balcony and saw the plane spinning. Within seconds, I realised that it was not a normal movement for a plane."
Brazil's President, Luiz Inácio Lula da Silva, expressed solidarity with the families and friends of the victims at an event where he was speaking.
“I have to be the bearer of very bad news and I would like everyone to stand up so that we can have a minute of silence," he told his audience.
He posted on social media that news of the crash was “very sad". "All my solidarity to the families and friends of the victims,” he said.
São Paulo's state Governor, Tarcísio Gomes de Freitas, has declared three days of mourning.
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