The airline Gol said in a statement that rescue teams on Tuesday found the bodies of the pilot and the copilot. The National Agency of Civil Aviation (ANAC,) which is leading the investigation, said they were found inside the plane's cabin.
Budget airline Gol's large Boeing 737-800 collided with a smaller, twin-engine private Embraer Legacy Friday. The Brazilian-built Embraer managed to land in a nearby military airfield, and its seven occupants were unhurt.
Brazilian Air Force commander brigadier Luiz Carlos da Silva Bueno indicated that the 100 bodies were found close to each other about one kilometre away from the landing-gear, in a remote area of dense Amazon rainforest in the state of Mato Grosso.
On Monday, the two black boxes of the Boeing, considered vital to the crash investigation, were found. Bueno said the boxes are in Brasilia and are to be sent to the United States in order to be studied by Boeing technical teams.
The black box of the Brazilian-built Legacy is being subjected to investigation in the town of Sao Jose dos Campos, in the state of Sao Paulo.
The US National Transportation Safety Board has sent three investigators to assist in the probe, and representatives of the US Federal Aviation Administration and Boeing Aircraft Company were also heading to the accident scene, a NTSB official said.
A key issue in the investigation is the possibility that one airplane was flying at lower or higher than it should have.
Under standard rules governing the Brasilia-to-southern-Amazonia airspace, planes flying north to south such as the Boeing are to fly at an odd altitude, in this case 37,000 feet (11,300 metres,) Bueno explained. Planes going in the opposite direction, such as the Embraer, are to keep to an even altitude, at 36,000 feet (10,900 metres.)
Legacy pilot Joseph Lepore - a US national whose passport has been reportedly confiscated by Brazilian officials - confirmed in a statement to Brazilian aeronautical authorities that the small plane was flying at 37,000 feet, according to civilian police in the state of Mato Grosso where the crash occurred.
That would have violated the airspace rules.
'Someone must have changed the original plan,' the Air Force commander said,
The Brazilian daily O Globo reported that on Monday a judge ordered the confiscation of the passports of both the US pilot and copilot, both of them American.
The Brazilian Air Force (FAB) sent further personnel to the site of the crash, in order to accelerate a rescue operation that was hampered by bad weather on Tuesday.
Rescue teams are cutting through thick jungle vegetation. The human remains are being taken to Brasilia for identification.
Families of the victims have flown over the site of the crash and were 'impressed' with the difficulty of the rescue operation, Bueno noted.
A full probe into the mishap is expected to take at least three months, given the difficulty of reaching the remote jungle crash site. The wreckage was not found until Saturday.
In the US on Tuesday, The New York Times published an account of the miraculous survival of the Legacy by one of its business writers.
Joe Sharkey described the tense moments as the plane recovered, and how some of the seven men on board started writing letters to loved ones. After the plane landed safely, the passengers 'bowed our heads in a long moment of silence, with the sound of muffled tears' when they learned that a Brazilian airliner with 155 people aboard was missing after Friday's mishap.
Sharkey, a weekly columnist for the Times business-travel section, wrote that the US pilots of the Embraer were stunned by the fate of the other aircraft. It was 'clear the weight of all this would remain with them forever,' he wrote.
