Joseph Lepore, the pilot, and Jan Paladino, his co-pilot, were at the controls of a newly-built Embraer Legacy 600 jet when it collided with a Boeing 737 at 11,200m (37,000ft) on Friday, allegedly sending the larger plane spiralling to the floor of the Amazon rainforest, resulting in the deaths of all 155 passengers and crew on board.

Miraculously, the seven passengers on board the Legacy jet – all American – survived after their plane was able to land safely at a nearby air force base.

Judge Tiago de Abril in Mato Grosso state, where the Boeing 737 went down, said that police had seized the passports of Mr Lepore and Mr Paladino, both US citizens, as a "cautionary" measure while the investigation was proceeding.

But Maria Barbant, spokeswoman for the State Justice Department said that officials had acted "as a result of the doubts surrounding the case and the emergence of indications that the accident was caused by the Legacy."

She said the two were not arrested but "just prevented from leaving the country, at least until we know exactly what happened."

The two pilots arrived yesterday in Rio de Janeiro for medical and psychological tests as part of the enquiry. They face more questioning today. "They are being interviewed by the authorities and are giving their total cooperation with the investigation," said Glauco Paiva, a US consulate official in Rio.

Mid-air collisions are extremely rare, and authorities are investigating why anti-collision devices, which were fitted on to both planes, were not able to prevent the crash, which marks Brazil's worst ever aircraft disaster.

Investigators are said to believe that both planes should have been flying at different altitudes and that human error, by the Legacy jet’s pilots as well as air traffic controllers, resulted in the Legacy flying towards the jungle city of Manaus at 37,000ft rather than 36,000ft.

That is the altitude reserved for planes from Manaus to Brasília — the Boeing’s origin and destination, en route to Rio de Janeiro.

When air traffic control realised the problem it could not contact the Brazilian-made Legacy, which was in an area over the rainforest where controllers cannot contact planes by radio.

However, yesterday O Globo, a daily Brazilian newspaper, reported that Legacy disobeyed an order by the control tower to descend to a lower altitude just before coming into contact with the larger aircraft.

Investigators are also trying to determine why the corporate jet survived while the more powerful Boeing 737, operated by the Brazilian carrier Gol, crashed. One theory is that the Gol pilot may have swerved at the last minute to avoid the Legacy, sending his plane into a deadly dive.

Yesterday one of the passengers aboard the private jet described the terrifying moments after the plane was struck by the Boeing 737, clipping a wing and spinning the aircraft out of control.

Joe Sharkey, a New York Times journalist who was on a freelance assignment for the aviation magazine Business Jet Traveller, told of his extraordinary brush with death as the pilots began a desperate struggle to bring the plane under their command, and of the heartache after learning the fate of the passengers on the Boeing 737.

Writing in his newspaper, Mr Sharkey described the instant his flight went horribly wrong: "Without warning, I felt a terrific jolt and heard a loud bang, followed by an eerie silence, save for the hum of the engines. I lifted the shade. The sky was clear; the sun low in the sky. The rainforest went on for ever. But there, at the end of the wing, was a jagged ridge, perhaps a foot high, where the five-foot-tall winglet was supposed to be."

As he stared out of the window it became clear that the situation was worsening. Rivets started to come loose and the edge of the wing began to peel back. The plane started to lose speed.

The pilots, whose calm in the crisis was praised by Mr Sharkey, scanned maps and searched for a landing place in what is one of the world’s most isolated regions. "By now we all knew how bad this was. I wondered how badly ‘ditching’ — an optimistic term for crashing — was going to hurt. I thought of my family. And as our hopes sank with the sun, some of us jotted notes to spouses and loved ones and placed them in our wallets, hoping the notes would later be found."

Then the pilots spotted a Brazilian air force base hidden in the jungle and managed to make an emergency landing. Several hours after their own near-brush with death, jokes about the close call turned to tears as Mr Sharkey and his fellow travellers were told of the Boeing’s fatal crash.

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