However it is unlikely that the Ducati star will be forced to pull out of his home grand prix at Phillip Island in two weeks.
Stoner has revealed he is riding in some pain due to an old scaphoid injury which will almost certainly require an operation.
He is battling to compete in the remaining races on the calendar - Japan, Australia, Malaysia and Valencia.
But he is likely to miss key pre-season tests for the 2009 season if he is recovering from surgery.
Stoner has virtually conceded his world title to Valentino Rossi after falling 87 points behind the Italian, who could wrap up his sixth premier class title at Motegi next weekend.
Stoner suffered the injury during a fall in 2003 and the fracture has failed to heal properly.
Stoner admitted that he was below form due to the problem at the recent Indianapolis Grand Prix in the US and said an operation was a probability.
"I'm not 100 per cent but I've got a few weeks to try and improve a few things," Stoner told the official MotoGP website.
"I do need an operation, but we'll race for as long as we can and try and do it at the end of the season.
"I don't think that we will do the tests at the end of this year - maybe Valencia but I'm not sure."
Ducati team boss Livio Suppo said Stoner's immediate future would depend on the extent of the pain and conceded he may not be able to complete the season.
"Let's say that at the moment, it is a problem in the races for Casey," Suppo said.
"He doesn't speak too much about it, but we will be taking things race-by-race.
"If the pain is manageable then he will finish the season. Otherwise we will try and get something arranged earlier.
"At the moment it seems that he will be able to complete the year, but if he is operated on after Valencia then he will definitely miss the Jerez test.
"That's not a big issue as he doesn't need a lot of tests in which to understand the bike," he said.
Stoner has battled injury worries from the start of his entry into MotoGP.
A six-year-old shoulder injury upset his preparations for his debut year in the class in 2006 and required surgery.
At the start of this year he crashed at Jerez, injuring his collarbone and missing several of the official scheduled tests.
Stoner has revealed he is riding in some pain due to an old scaphoid injury which will almost certainly require an operation.
He is battling to compete in the remaining races on the calendar - Japan, Australia, Malaysia and Valencia.
But he is likely to miss key pre-season tests for the 2009 season if he is recovering from surgery.
Stoner has virtually conceded his world title to Valentino Rossi after falling 87 points behind the Italian, who could wrap up his sixth premier class title at Motegi next weekend.
Stoner suffered the injury during a fall in 2003 and the fracture has failed to heal properly.
Stoner admitted that he was below form due to the problem at the recent Indianapolis Grand Prix in the US and said an operation was a probability.
"I'm not 100 per cent but I've got a few weeks to try and improve a few things," Stoner told the official MotoGP website.
"I do need an operation, but we'll race for as long as we can and try and do it at the end of the season.
"I don't think that we will do the tests at the end of this year - maybe Valencia but I'm not sure."
Ducati team boss Livio Suppo said Stoner's immediate future would depend on the extent of the pain and conceded he may not be able to complete the season.
"Let's say that at the moment, it is a problem in the races for Casey," Suppo said.
"He doesn't speak too much about it, but we will be taking things race-by-race.
"If the pain is manageable then he will finish the season. Otherwise we will try and get something arranged earlier.
"At the moment it seems that he will be able to complete the year, but if he is operated on after Valencia then he will definitely miss the Jerez test.
"That's not a big issue as he doesn't need a lot of tests in which to understand the bike," he said.
Stoner has battled injury worries from the start of his entry into MotoGP.
A six-year-old shoulder injury upset his preparations for his debut year in the class in 2006 and required surgery.
At the start of this year he crashed at Jerez, injuring his collarbone and missing several of the official scheduled tests.
AAP
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