Wallabies linchpin Stephen Larkham's World Cup campaign is in turmoil again after suffering a "freak" infection following knee surgery.

In a major blow to Australia's title hopes, Larkham has undergone another arthroscopy and has been ruled out of their next two matches.

At best he will return in time for a possible semi-final clash against the All Blacks but may have to come off the bench.

The 102-Test veteran, currently on a drip, will remain in hospital for another day or two after having surgery.

The symptoms of the infection flared on Tuesday when he was due to resume running in a bid to return off the bench against Canada.

"We hope he will be out (of hospital) tomorrow but he definitely won't be considered for this weekend or the following weekend," coach John Connolly said.

"He got up yesterday morning to start running. It was sore and it as just the start of an infection and he spent the night in there getting treated.

"He's very disappointed obviously, he was coming along quite well.

"It was one of those freak accidents."

Wallabies medical officer Dr Martin Raftery explained the infection was an unlucky result of Larkham's initial arthroscopy in Montpellier on September 16 to remove a floating bone fragment.

While the infection was external, between the skin and the knee capsule, fluid needed to be flushed through the knee to ensure the infection hadn't penetrated the joint's casing.

"It's a recognised complication of surgery and whenever you do any surgery one of the risks is infection," Dr Raftery said.

"You have bugs on your skin and when you insert a foreign instrument into your body you can take those bugs through to your knee joint and that's what's happened.

"It's just unlucky."

Dr Raftery said it was difficult to form a proper prognosis but confirmed a semi-final return was a best-case scenario.

Larkham has not trained since September 14 and probably won't resume running for more than a week.

Connolly had planned to play him off the bench against the Canucks with the view to starting the 33-year-old in the October 6 quarter-final in Marseille.

Now he must rely upon rookie Berrick Barnes to carry a huge load through to the semi-finals.

Barnes has already responded brilliantly to one pressure-filled assignment when he stepped in at five-eighth against Wales with only half a day's notice.

"It's a big challenge. He's still learning the position but mentally he handles things very well and he's got the all-round game to be a good Test player," Connolly said.

"The opportunity came for Berrick and he stepped up to the mark and played very well and we hope he keeps improving, that's the way you have to approach it."

Barnes is carrying a corked thigh injury but trained.

Connolly admitted it was an option to rest the 21-year-old from Saturday's clash in Bordeaux as a safeguard.

Versatile backs Julian Huxley and Matt Giteau could fill the role.

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