The winglet of the Legacy sliced off about half of the 737's left wing, causing the 737 to break up and crash into an area of dense jungle, killing all 154 passengers and crew on board.

CENIPA concluded that the accident was caused by air traffic control (ATC) errors, combined with mistakes made by the American pilots on the Legacy, including a failure to recognize that their traffic collision avoidance system (TCAS) was not activated, while the NTSB determined that both flight crews acted properly and were placed on a collision course by ATC, deeming the Legacy pilots' disabling of their TCAS system to be only a contributing factor rather than a direct cause.

The Boeing 737 eventually crashed into an area of dense rainforest, 200 kilometres (124 mi; 108 nmi) east of the municipality of Peixoto de Azevedo.

[1]: 137 [27][note 3] With radio relay assistance from Polar Air Cargo Flight 71, a Boeing 747 cargo aircraft flying in the area at the time, the Embraer's crew successfully landed the crippled jet at Cachimbo Airport, part of the large military complex Campo de Provas Brigadeiro Velloso, at about 160 kilometres (100 mi; 90 nmi) from the collision point.

Passenger and journalist Joe Sharkey described his experience on board the Embraer in an article for The New York Times, titled "Colliding With Death at 37,000 Feet, and Living", filed on 1 October 2006:[17]And it had been a nice ride.

The request, made by the Peixoto de Azevedo prosecutor,[31] was granted by Judge Tiago Sousa Nogueira e Abreu, who stated that the possibility of pilot error on the part of the Embraer crew could not be ruled out.

[32] The Embraer crew was forced to remain in Brazil until their passports were released to them on 5 December 2006, more than two months after the accident, after federal judge Candido Ribeiro ruled no legal grounds existed for "restricting the freedom of motion of the foreigners.

"[33][34] Prior to their scheduled departure to the United States, the crew was formally charged by Brazilian Federal Police with "endangering an aircraft", which carries a penalty up to 12 years in prison.

They picked up their passports and flew back to the U.S.[36][37] The Brazilian Air Force (the Força Aérea Brasileira or "FAB") sent five fixed-wing aircraft and three helicopters to the region for an extensive search and rescue (SAR) operation.

[38] The crash site of Gol Flight 1907 was spotted on 30 September by the air force, at coordinates,[39] 200 kilometres (120 mi; 110 nmi) east of Peixoto de Azevedo, near Fazenda Jarinã, a cattle ranch.

[43] The FDR and a nondata part of the cockpit voice recorder (CVR) from the Boeing 737 were found on 2 October 2006 and handed over to the investigators, who sent them to the TSB for analysis.

[note 4][28][45] On 25 October 2006, after nearly four weeks of intensive searching in the jungle by about 200 Brazilian Army troops equipped with metal detectors, the memory module of the Boeing's cockpit voice recorder was found.

According to the filed flight plan, the Embraer was scheduled to have been level at FL380, proceeding towards Manaus, while passing the eventual collision point, which was about 307 kilometres (191 mi; 166 nmi) northwest of Teres.

[citation needed] The Embraer's crew asserted in their depositions and subsequent interviews that they were cleared by ATC to FL370 for the entire trip, all the way to Manaus.

[1]: 40 At 16:59:50, about three minutes after the collision, Amazonic Center started to receive the Embraer's secondary radar reply, with its correct altitude and last assigned code.

[52] The NTSB reported that the Embraer apparently experienced a TCAS outage, unknown to its flight crew prior to the collision, according to the CVR: Preliminary findings in the ongoing investigation indicate that for reasons yet to be determined, the collision avoidance system in the Legacy airplane was not functioning at the time of the accident, thereby disabling the system's ability to detect and be detected by conflicting traffic.

The NTSB added that the design of the Embraer's avionics is such that the nonfunctioning of the TCAS that apparently occurred is shown by a small static white text message, which may not be noticeable by the flight crew.

The NTSB noted:Using only static text messages to indicate a loss of collision avoidance system functionality is not a reliable means to capture pilots' attention because these visual warnings can be easily overlooked if their attention is directed elsewhere in the flight environment.Based on its observations, the NTSB recommended to the FAA that design changes be implemented to improve the noticeability of TCAS announcements, and that the FAA advise pilots of all aircraft types to familiarize themselves with the details of this accident, with the ways in which a pilot could inadvertently cause the loss of transponder and/or TCAS function, and how to recognize a loss of function.

[1] The CENIPA report includes a "Conclusions" section that summarizes the known facts and lists a variety of contributing factors relating both to air traffic controllers and to the Legacy jet's flight crew.

[54][55] According to CENIPA, the air traffic controllers contributed to the accident by originally issuing an improper clearance to the Embraer, and not catching or correcting the mistake during the subsequent handoff to Brasília Center or later on.

[1]: 41 [55] CENIPA concluded that the ExcelAire pilots also contributed to the accident with, among other things, their failure to recognize that their transponder was inadvertently switched off, thereby disabling the collision avoidance system on both aircraft, as well as their overall insufficient training and preparation.

The loss of effective air traffic control was not the result of a single error, but of a combination of numerous individual and institutional ATC factors, which reflected systemic shortcomings in emphasis on positive air traffic control concepts.The NTSB further added these contributing factors: Contributing to this accident was the undetected loss of functionality of the airborne collision avoidance system technology as a result of the inadvertent inactivation of the transponder on board N600XL.

"[4] Aviation Week adds that "the Brazilian military operates that country's air traffic control system, conducted the investigation, and authored the report.

[67][68] Amid rising tensions, the air traffic controllers began staging a series of work actions, including slowdowns, walkouts, and even a hunger strike.

This led to chaos in Brazil's aviation industry – major delays and disruptions in domestic and international air service, stranded passengers, cancelled flights, and public demonstrations.

[69] On the same day, Lula appointed former Supreme Court president Nelson Jobim to replace Pires, and vowed to improve Brazil's ATC system.

The attorney representing the Embraer crew, Miami-based Robert Torricella, responded to the allegation that the crew was flying at an "incorrect altitude" by stating that according to international regulations, clearances and directives issued by ATC supersede a previously filed flight plan, and in this case:[74]... the flight plan cleared by air traffic control at the time of departure required the Embraer to fly all the way to Manaus at 37,000 feet, and absent contrary directives from air traffic control, the Embraer was obligated to follow its cleared flight plan.

[73][76] On 1 June 2007, Murilo Mendes, a Brazilian federal judge in the small city of Sinop, Mato Grosso, near the crash site of the Boeing, indicted the two Embraer pilots and four Brasília-based air traffic controllers for "exposing an aircraft to danger.

[87] On that date, the court upheld the prior convictions, but modified the sentences to 37 months for each, requiring that the pilots "report regularly to authorities and stay home at night.

[94] The Mato Grosso midair collision was featured in the 2008 episode "Phantom Strike", of the Canadian-made, internationally distributed documentary series Mayday[41] The collision was also one of the incidents included in the 2009 episode "System Breakdown", of the Mayday special series Science of Disaster, which examined the role of air traffic controllers in aviation disasters.