Benoit Pedretti is to undergo surgery on the groin problem which has ended his 2010/11 campaign.
Auxerre have already accepted that their skipper will not figure again this season, with the France international having suffered a setback in his recovery from a previous injury.
The midfielder's absence has dealt a heavy blow to the club's efforts to beat the drop, but they appreciate that Pedretti must get to the bottom of the issue.
Auxerre coach Jean Fernandez has confirmed that the 30-year-old will go under the knife at some point this week.
"Despite all the care he has received in recent weeks, Benoit struggled when running," he said.
"A decision has been made, with the help of the medical staff, that surgery is unavoidable.
"He will undergo surgery in Lyon and his season is therefore over.
"I was counting on his return for the final stretch of the season. We really didn't need this now. His absence will seriously complicate the end of our season."
Pedretti's injury setback has not stopped reports in France from linking him with a summer switch to Lille.
The Ligue 1 leaders have done little to play down the speculation, but they have been quick to point out that no deal is in place.
"Pedretti is one of the players we are following but there are no agreements with anyone for next season," said Lille's vice-managing director Frederic Paquet.
"We have not yet finished with our efforts to extend the deals of those players we want to keep at the club."