[12] The Australian Transport Safety Bureau (ATSB) investigation found a fault with one of the aircraft's three air data inertial reference units (ADIRUs) and a previously unknown software design limitation of the Airbus A330's fly-by-wire flight control primary computer (FCPC).

At 12:42:27, the aircraft made a sudden, uncommanded pitch-down manoeuvre, experiencing −0.8 g,[note 1] reaching 8.4 degrees pitch down and rapidly descending 650 feet (200 m).

[16][17] Unrestrained (and even some restrained) passengers and crew were flung around the cabin or crushed by overhead luggage, as well as crashing with and through overhead-compartment doors.

The pilots stabilised the plane and declared a state of alert, which was later updated to mayday when the extent of injuries was relayed to the flight crew.

[19][20] On 15 January 2009, the European Aviation Safety Agency (EASA) issued an emergency airworthiness directive[21] to address the problem of A330 and A340 aircraft, equipped with the Northrop-Grumman ADIRUs, incorrectly responding to a defective inertial reference.

The aircraft was fitted with three ADIRUs to provide redundancy for fault tolerance, and the FCPCs used the three independent AOA values to check their consistency.

Overall, the design, verification and validation processes used by the aircraft manufacturer did not fully consider the potential effects of frequent spikes in data from an ADIRU.

The FCPC then processed the erroneously high AOA data, triggering the high-AOA protection mode, which sent a command to the electrical flight control system to pitch the nose down.

A much more likely scenario was that a marginal hardware weakness of some form made the units susceptible to the effects of some type of environmental factor, which triggered the failure mode.

[14] Although speculation arose that interference from Naval Communication Station Harold E. Holt or passenger personal electronic devices could have been involved in the incident, the ATSB assessed this possibility as "extremely unlikely".

[14] The ATSB's final report, issued on 19 December 2011, concluded that the incident "occurred due to the combination of a design limitation in the FCPC software of the Airbus A330/A340, and a failure mode affecting one of the aircraft’s three ADIRUs.

The design limitation meant that in a very rare and specific situation, multiple spikes in AOA data from one of the ADIRUs could result in the FCPCs commanding the aircraft to pitch down.

[24] The incident again fuelled media speculation regarding the significance of the aforementioned Harold E. Holt facility, with the Australian and International Pilots Association calling for commercial aircraft to be barred from the area as a precaution until the events could be better understood,[25][26] while the manager of the facility claimed that it was "highly, highly unlikely" that any interference had been caused.

Further compensation claims would be considered on a case-by-case basis,[29] with several passengers from the flight pursuing legal action against Qantas.

[30][31] Permanently injured flight attendant Fuzzy Maiava was advised not to take an NZ$35,000 compensation payment from Qantas so that he could take part in a class-action lawsuit against Airbus and Northrop Grumman.