Evasive action had to be taken by the pilots of two Qantas aircraft over Adelaide when the planes flew into each other's airspace.

The Australian Transport Safety Bureau (ATSB) says the incident occurred over Gulf St Vincent, about 20 kilometres west of Adelaide, about lunchtime on Friday (ACST).

The Civil Aviation Safety Authority (CASA) confirmed the apparent "near miss" and said the pilots had to take evasive action.

Qantas confirmed two of its Airbus A330 aircraft were involved, but denied it was a near-miss.

The airline says an onboard alert allowed the pilots to overcome a "loss of separation" between the aircraft.

What is a "loss of separation"? Separation is the idea of keeping aircraft a minimum distance from each other at all times, to remove the risk of a collision.

is the idea of keeping aircraft a minimum distance from each other at all times, to remove the risk of a collision. A loss of separation incident means air traffic controllers were unable to guarantee the minimum separation distance between two aircraft could be maintained.

A incident means air traffic controllers were unable to guarantee the minimum separation distance between two aircraft could be maintained. Read more about Australia's air traffic control system.

"Indications are that the loss of separation occurred when one of the Qantas aircraft received clearance to climb from air traffic control," a statement from Qantas said.

"Our pilots followed standard operating procedures in re-establishing the required separation distance following the alert from the onboard notification system.

"There was no impact to passengers."

The ATSB says it will review flight and cockpit recordings from the two aircraft, as well as interview all the pilots and air traffic controllers.

The bureau says controlled airspace requires planes to be 1,000 feet apart vertically and five nautical miles horizontally.

An air traffic controller has been stood down, which is standard procedure when an incident is under investigation.

Passengers describe 'dropping down' sensation

One flight had been heading from Sydney to Perth (QF581), and the other from Perth to Sydney (QF576).

The ATSB says QF576 was flying at 39,000 feet when QF581 was given clearance to climb from 38,000 feet to 40,000 feet.

The pilots of the Sydney-bound flight received an onboard alert from their collision avoidance system and traffic control cancelled the clearance to climb, the bureau said.

Passenger Janet McLean was on the plane that arrived in Sydney and says she did not think there was a major issue during the flight.

"There was a sensation of certainly dropping down, like one drop and then another drop and then we must have just levelled back out," she said.

"I sort of thought, I presumed, an air pocket - but it really wasn't bumpy like an air pocket, it was a smoother sort of drop.

"Apart from that, no, we had a beautiful landing and the crew were all fine and we certainly didn't think of anything else."

A passenger onboard the flight from Sydney to Perth says he saw the other plane flying below.

Gary Martin says Qantas staff did not say anything about the incident and he was not concerned.

"I saw a plane going underneath us to the left, somewhere in South Australia I'd suggest," he said.

"I don't think anybody knew, I saw it and didn't care. They know what they're doing."

Walter Bird said he did not notice any unusual moves or violent changes.

Other passengers said it seemed like a normal flight and Qantas staff did not tell them anything.