Gol Transportes Aéreos Flight 1907 crashed 1,750km (1,100 miles) north-west of Rio de Janeiro killing all people onboard, on Friday September 29. National Civil Aviation Agency (ANAC) has confirmed that the crashed Brazilian airplane did crash into a smaller aircraft. Rescue workers and air force personnel are searching the wreckage for bodies 
Search and rescue teams rappelled down ropes or hacked a way through the rainforest, led by local Indians to reach the wreckage.
The first people at the scene had to abseil down to clear away trees to allow helicopters to land.
"It's extremely difficult to get there," said Ademir Ribeiro, a foreman on the nearby Jarina ranch, the centre for rescue operations.
About 80 air force personnel were at the site during the day and about thirty stayed during the night. 
An air force statement says that the first two bodies were recovered on the afternoon of Sunday, October 1. The bodies were taken to an air force base by helicopter. 
Officials say that the investigation would take at least three months. Milton Zuanazzi, director of the National Civil Aviation Agency, says that he does not know how long the removal of bodies would take.
A Embraer Legacy 600 owned by ExcelAire, a charter company based in Long Island, New York clipped the Boeing 737-800 SFP. The Legacy made an emergency landing at Cachimbo air force base with five passengers and two crew on board, none of whom were hurt. The Boeing plunged nose first into the rainforest and disintegrated. 
When interviewed by the police, the passengers on the Legacy reported feeling a bump at the time of the collision. The pilot landed the plane manually. 
An Air Force statement said that a search of the site showed no signs that the 149 passengers and six crew on board the Boeing 737 could have survived the crash.
"Neither of the pilots can understand how a 737 could have hit us without them seeing it," said Joe Sharkey, a journalist for the New York Times, in an email to his wife. 
Mr. Zuanazzi says it's possible as they were traveling at hundreds of miles an hour.
"They said they didn't see anything. But this is absolutely normal.  …In these conditions, you can only see a shadow and a noise," said Zuanazzi.
Investigators are trying to determine why two new aircraft equipped with the latest anti-collision technology could have collided. The Brazilian air force says that both planes were equipped with a Traffic Collision Avoidance System (TCAS) which sounds an alarm when planes get too close.
"It locks on the other plane's transponders and tells the pilot whether to go up or down," John Hansman, aeronautics professor at the Massachusetts Institute of Technology, said by telephone.
"The 737 should have been warned to take evasive action."
Hansman said that in air traffic in Brazil is complicated in some parts and vast areas are not covered by radar especially over the ocean on the Amazon Rainforest. Pilots often propose a route and at certain points check with controllers who verify the plane's location, altitude and bearing.
"Apparently that process broke down somehow," Hansman said.  "When you get to the jungles of Brazil, you have people going in all directions."
The Brazilian mass communications media are suggesting that a lapse in communication caused the crash. Rio de Janeiro daily O Globo reported that air traffic controllers in the city of Manaus cleared the Boeing to fly at 37,000 feet and Brasília authorised the Legacy to climb from 35,000 feet to 39,000 feet.  Agência Estado reports the Legacy pilot Joseph Lepore and co-pilot Jan Palladino told police in Mato Grosso that they had authorisation from Brasília to fly at 37,000 feet and that the anti-collision equipment never sounded a warning.
The cockpit voice recorder and the digital flight data recorder of both planes have been recovered. The blackbox of the Legacy was taken to Embraer's headquarters at Sao Jose dos Campos, Sao Paulo.
Brazil's Civil Aviation Agency said the cause of the crash was impossible to say until the Boeing 737's two recorders, found by search teams, were examined.
Dale Oderman, associate professor of aviation technology at Purdue University said investigators will be paying close attention to the conversations between the pilots and air traffic controllers said.
"It might indicate they were flying an altitude they weren't cleared to fly," Mr. Oderman said.
Bill Waldock, aviation safety professor at Embry-Riddle Aeronautical University in  Prescott, Arizona, says that the Legacy may have clipped the bigger jet's horizontal stabiliser — fins that prevent the airplane from pitching up or down.
"A likely reason why the 737 would depart continuous flight and go vertically into the jungle at that speed would be damage or loss of the horizontal stabiliser," Mr. Waldock said.
Relatives of the passengers have complained that they were not being informed about the ongoing search for bodies or the investigation. The air force has flown them in groups of six over to the crash site. The air force says that it was to show them how difficult it is to reach the crash site.
"They will be able to see the difficulties of the operation...  The place is difficult [to access], there are trees of up to 40 meters (130 feet) tall," a spokesman said.  "The debris is scattered so rescue work is even more complicated."
This is the worst air disaster in Brazilian history, surpassing the June 1982 crash of a VASP flight which hit a mountain near Fortaleza in northeastern Brazil, killing 137 people.
President Lula has declared three days of national mourning.
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Rescue workers search wreckage of Brazilian air crash