The controversy about the cause of the crash began immediately, when the Accident Investigation Committee (Junta Investigadora de Accidentes, JIA) of the Ecuadorian Air Force attributed the crash to pilot error, supposedly caused by an overloading with cargo. The parliamentary commission formed months after, after pressure from the families of the victims and political groups allied with the president, found contradictions and inconsistencies in the JIA report, but could not reach definitive conclusions especially since the aircraft that was purchased by the Air Force to operate as a VIP transport lacked the Flight Data Recorder equipment (Black Box). The Zurich Police, who also conducted an investigation, concluded that the plane's motors were shut down when the plane crashed into the mountain. This opinion, which contradicted the Air Force Report, was not investigated further by the Ecuadorian government.
The American author and activist John Perkins, in his book Confessions of an Economic Hit Man, concludes that Roldós was assassinated, allegedly by a bomb located in a tape recorder, because his plan to reorganize the hydrocarbon sector would have threatened U.S. interests. Roldós had entered into a pact with neighboring Colombia and Peru, a pact which US President Reagan saw as a tilt toward the Soviet Union. Just months after Roldós died, another Latin American leader who had been at odds with U.S. interests in the control of the Panama Canal, Panama's Omar Torrijos, died in what was allegedly just a plane crash, which also is perceived by some to have been a CIA-conducted assassination,