If convicted of exposing an aircraft to danger, the two could face up to 12 years in prison, Brazilian federal police said.
Joseph Lepore, 42, of Bay Shore, N.Y., and Jan Paladino, 34, Westhampton Beach, N.Y., were questioned Friday by police for six hours and then allowed to pick up their passports and leave the country. They are required to return to Brazil for their trial.
Lepore and Paladino were piloting a Brazilian-made Legacy executive jet on Sept. 29 when it collided with a Gol Airlines Boeing 737-800 heading south over the Amazon jungle. All 154 people aboard the Gol flight were killed, while the Legacy landed safely with all seven people aboard unharmed.
Police filed the accusation because "elements and evidence in the investigation indicated a lack of caution necessary and expected from pilots during flight," police said in a statement.
Under Brazilian law, a judge will now decide whether to indict the pilots and send them to trial, a process that could take weeks or months.
Police said Lepore and Paladino told them they would respond to the accusations in court. Their attorney said they were notified of the allegations when they walked into Friday's meeting with police.
"The decision of this investigator to accuse Joe and Jan of a crime without ever hearing their testimony is incredibly absurd," said the attorney, Robert Torricella.
The Legacy, owned by ExcelAire of Ronkonkoma, N.Y., was heading northwest on its maiden voyage from the southern city of Sao Jose dos Campos to the United States when the accident occurred at 37,000 feet, an altitude usually reserved for flights headed in the opposite direction.
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. The pilots have denied any wrongdoing.
There is "no question they had permission to be at 37,000 feet," Torricella said. "They were never given a contrary instruction."
Warning systems failed on both planes before they collided, an Air Force investigator said last month.
Brazilian authorities seized the pilots' passports after the crash to prevent them from leaving the country, and they had been staying in a hotel on Rio's Copacabana Beach. A court released their passports this week, saying there were no legal grounds for restricting their movements.
Another lawyer for the pilots, former Justice Minister Jose Carlos Dias, said Lepore and Paladino 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.