The pilot of a Qantas cargo flight from Brisbane to Melbourne made an emergency landing in Canberra on Wednesday after his co-pilot became incapacitated.

A fault in the aircraft's air control system caused the cabin to lose air pressure, forcing the crew to wear oxygen masks and immediately descend to 20,000 feet.

In the air traffic control audio recording, the pilot can be heard declaring mayday while breathing through his oxygen mask.

The plane involved was a Boeing 737-300 which was converted into a cargo aircraft in 2003. Prior to that, it had been operated as a commercial passenger plane by Qantas in New Zealand.

In the audio, the pilot can be heard asking for the weather conditions in Canberra as "they had to get on the ground immediately", then telling controllers to arrange for ambulance staff to meet the flight when it landed in Canberra.

The pilots were taken to hospital as a precaution.

The Australian Transport Safety Bureau has launched an investigation.

Newshub.