Australia scrumhalf Will Genia has undergone a full reconstruction of his right knee after rupturing his anterior cruciate ligament during the Wallabies' 26-19 defeat of South Africa over the weekend.

The surgery at a Brisbane clinic went well, but Genia's expected recovery time remained a minimum six months, the team said in a statement.

The Papua New Guinean-born 24-year-old, rated one of the finest scrumhalves in the world, has been replaced by Nick Phipps for the Wallabies' first match of the tournament against Argentina in the Gold Coast on Saturday.

Australia lost both their opening matches to New Zealand and lie third in the four-team southern hemisphere competition, eight points behind the leading All Blacks.