Walton, named a Living National Treasure by the National Trust of Australia in 1997, died from natural causes, The Australian reported.
Walton learned to fly at age 17 and two years later became the first woman in Australia to obtain a commercial pilot's license.
Last October, she attended inaugural ceremonies for Qantas' first super passenger jet, an A380 Airbus named in her honor.
"I was asked if Qantas could name this plane after me at my 90th birthday three years ago and I made it my decision to stay alive," Walton said at the ceremony in Sydney.
Walton pioneered an air ambulance service for the Australian Outback, was commandant of the Women's Air Training Corps from 1940 to 1945, and founded the Australian Women's Pilot Association.
Walton is survived by her daughter, Anne Marie, her son John, four grandchildren and two great-grandchildren.