Kurt Fearnley had just crawled along a 60-mile jungle track in Papua New Guinea.
But when he arrived at Brisbane airport a few days later, Jetstar— an offshoot of Qantas airlines — asked him to check in his wheelchair.
The Australian budget airline offered him its own wheelchair, specially designed for planes, but told Fearnley he would have to be pushed by airline staff.
Fearnley, who won marathon gold in the Beijing and Athens Paralympics, was insulted at being asked to give up his independence.
He said the equivalent for an able-bodied person "would be having your legs tied together, your pants pulled down and be carried or pushed through an airport."
In protest, he rejected the airline's wheelchair and dragged himself through the terminal, in and out of the toilet, and onto the plane.
Jetstar has now issued an apology, saying any embarrassment and hurt was not intentional.
It said its policy for passengers in wheelchairs was for them to transfer to the airline wheelchair, which is more maneuverable on the plane, at the boarding gate.
Jetstar have now assured Fearnley they are working on an alternative boarding procedure for disabled passengers.
He said: "As long as that's going ahead, I'm more than happy."
Since the incident, a man from Melbourne has said he spent six days in hospital after he fell out of a Jetstar wheelchair while being pushed by staff.