In a sombre ceremony, their flag-draped coffins were loaded onto Australian airforce planes by a military guard of honour as a bugle sounded the Last Post.
Australia sent more than 60,000 troops to fight in the Vietnam War and 521 were killed. Soldiers were buried in the nearest Commonwealth cemetery unless their families could pay for repatriation to Australia.
"As a soldier, I am proud that the remains can be brought closer to their loved ones," said Abdullah Sani Mohamed, the Army Museum Director, who oversees Terendak Military Cemetery in Malaysia, where the Australians were buried.
In 1966, Australia changed the repatriation policy so that all fallen soldiers would be taken home.
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Last year, the government offered to pay for the repatriation of any soldiers buried overseas prior to the policy change, with 33 families accepting the offer.
Another body will be repatriated from Kranji Cemetery in Singapore, the Australian government said in a statement.
The remains in Malaysia were driven from Terendak Military Cemetery to Subang Airbase, west of the capital Kuala Lumpur, in white vans early today.
Family members of the deceased, including Christopher Bowtell, whose grandfather Robert Walter Bowtell died in the Vietnam War, were at the event.
"He is finally coming home," Bowtell, who also serves in the Australian army, told AFP, adding that his family were "pretty excited -- it is going to be quite an experience".
The coffins will be flown to Richmond Royal Australian Air Force Base, where families of the servicemen and civilians will gather for a ceremony Thursday.