Transcripts suggest the Legacy had been authorized by the tower in Sao Jose dos Campos to fly at 37,000 feet to Manaus, although that contradicted the plane's original flight plan.
Warning systems failed on both planes before they collided, an Air Force investigator said last month.
Air traffic controllers believed the Legacy was flying at 36,000 feet at the time it collided with Gol Flight 1907, Brig. Gen. Luiz Carlos da Silva Bueno recently told a Senate committee.
But "at departure, air traffic control cleared the Legacy to Manaus at 37,000 feet," ExcelAire lawyer Robert Torricella said at the time. "Absent a contrary clearance by air traffic control, the Legacy was required to remain at that altitude."
The lawyer for the pilots, former Justice Minister Jose Carlos Dias, said the pilots picked up their passports and were taken to Guarulhos airport for a charter flight to the United States.
Dias called the police decision "biased" and "discriminatory," and said police were simply "looking for someone to blame for the crime." He added that if the factors leading to the fatal collision were considered unintentional, the maximum penalty would fall to four years in prison.
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