Police earlier seized the passports of pilots Joseph Lepore and Jan Paladino, both from New York State, to prevent them from leaving the country.
The two were piloting the Brazilian-made Embraer Legacy 600 when it collided with a Boeing 737-800 over Mato Grosso state in the Amazon rain forest. The Boeing crashed, killing all 155 aboard. The Legacy landed safely at an air force base.
"We have received an order from the Federal Prosecutor's Office in Mato Grosso to begin investigating the possible commission of a crime inside the aircraft," said Geraldo Pereira, acting director of the Federal Police in Mato Grosso, speaking by phone.
"We will start investigating if the two pilots caused the accident and if they are considered guilty they could be charged with involuntary manslaughter," Pereira said.
Investigators are puzzled why the pilots weren't alerted by equipment designed to avoid collisions. The air force said both jets were equipped with a traffic collision avoidance system, which monitors other planes and sets off an alarm if they get too close.
"Preliminary investigations indicate that the pilots may have turned off the transponder" that communicates the plane's location, he said. If so, that would mean "that they knew the risks they were running and nevertheless they took certain attitudes that endangered the lives of people."
The Brazilian newspaper O Globo reported on Tuesday that the Legacy, which was carrying seven Americans, disobeyed a control tower order to descend to a lower altitude before coming into contact with Gol airlines Flight 1907.
It said the Legacy flew at 37,000 feet to the capital Brasilia, but then ignored an order to descend to 36,000 feet to continue its flight to the Amazon city of Manaus. The Gol jetliner was flying at 37,000 feet from Manaus to Brasilia en route to Rio de Janeiro.
U.S. journalist Joe Sharkey, who was on the smaller plane, wrote in The New York Times that he visited the pilots shortly before the crash. He said they told him "the plane was flying beautifully" and he noted a display of the altitude read 37,000 feet.
A judge in Mato Grosso state, where the Gol plane crashed deep in the Amazon jungle, ordered police to seize the passports of Lepore and Paladino "as a result of the doubts surrounding the case and the emergence of indications that the accident was caused by the Legacy," state Justice Department spokeswoman Maria Barbant said.
She said the two were not arrested but "just prevented from leaving the country, at least until we know exactly what happened."
"They have been interviewed by Brazilian authorities and they have been thoroughly cooperating with them in the investigation," said Glauco Paiva, a spokesman for the U.S. consulate in Rio de Janeiro.
The Legacy was making its inaugural flight to the United States, where it had been purchased by ExcelAire Service Inc., based in Ronkonkoma, N.Y.
The company "has never been involved in an accident since its founding in 1985," ExcelAire spokeswoman Lisa Hendrickson said by phone on Wednesday. "Both pilots were captain-qualified to fly the Legacy."
The company said the jet lost its left winglet in the collision and received damage to the leading edge of the wing.
Hendrickson told Newsday that Lepore, a commercial pilot for more than 20 years from Bay Shore, N.Y., had logged more than 8,000 hours of flight time while Paladino, of Westhampton Beach, N.Y., has more than 6,400 hours of flight time and has been a commercial pilot for a decade, she said. Air force commander Gen. Luis Carlos Bueno said Gol's brand-new Boeing 737-800 had a flight plan for 37,000 feet, while the Legacy jet was authorized to fly at 36,000 feet, according to an interview Tuesday with Brazil's government news service Agencia Brasil.
He said neither plane was authorized to deviate from the plans. He said only an investigation of the planes' flight recorders could clarify the cause of the accident.
Neither the air force nor the National Civil Aviation Agency would comment to The Associated Press on the reports.
Christine Negroni, an investigator for the aviation law firm Kreindler & Kreindler of New York, said in an e-mail that under international guidelines, westbound planes are supposed to fly at even-numbered altitudes, and eastbound planes at odd-numbered altitudes, as measured in feet.
"Since the American pilots were flying northwest, they should not have been at 37,000 (feet), since that's odd," she said.
Investigators began examining voice and data recorders recovered from the jetliner Tuesday, but the National Civil Aviation Agency said one of the voice recorders was missing a database.
The Gol plane crashed deep in the Amazon jungle near Peixoto de Azevedo in Mato Grosso state, some 1,100 miles northwest of Rio de Janeiro, killing all 149 passengers and six crew members.
Among the dead was U.S. citizen Douglas Hancock, 35, of Missouri. He was in Mato Grosso for business and was returning to Rio de Janeiro where he lived, his father, Paul Hancock, told the Southeast Missourian newspaper.