An interim report has found a collision avoidance system was not working effectively on one of two Qantas aircraft involved in an incident over South Australia last month.

An Airbus A330 flying from Perth to Sydney went close to another travelling from Sydney to Perth.

The collision avoidance system on the Perth-Sydney plane activated but the report concluded the same system did not activate on the other Airbus.

Both aircraft landed safely.

The Australian and International Pilots Association said last month a collision warning alert was the last line of defence for pilots and its vice-president Richard Woodward said the planes might have been within a minute of hitting each other.

A full investigation is expected to be completed by next September.