The transport safety watchdog has confirmed it is analysing the autopilot system of QF72 as part of its investigation into why the Qantas airliner dropped nearly 1000 feet in two terrifying plunges earlier this week.

The Fairfax Media reported yesterday that Qantas insiders believed a problem with the autopilot system was linked to an apparent malfunction of the A330's vertical elevator.

The elevator device - which controls the aircraft's up-and-down movement - was highlighted by investigators on Wednesday as possibly contributing to the dramatic loss of altitude which left 15 people seriously injured.

The Australian and International Pilots Association president, Captain Ian Woods, backed the view that the autopilot system was involved, saying that - based on investigator's statements - a problem auto-flight control was "a likely explanation".

Australian Transport Safety Bureau investigations director, Julian Walsh today confirmed that investigators were focussing on the aircraft's autopilot system, as well as its flight control computers and the crew's interaction with them.

"The plane was on autopilot before the incident happened," Mr Walsh said.

"We will be investigating whether the autopilot switched off and at what point it switched off and why."

"At this point, the event appears very complex. The aircraft contains very sophisticated and highly reliable systems whose interaction is very complex. As far as we can understand, there seems to be issues with some on-board components."