Newcastle insist the injury is not serious and they expect Wilkinson to be available for the Guinness Premiership clash with Leeds on December 27.
"The injury is more commonly known as a sportsman's hernia, which is the same thing Alan Shearer had a few weeks ago," said Newcastle boss Rob Andrew.
"We are told it's a fairly routine operation, and we hope to have him back for the Premiership game against Leeds on December 27, all things being well."
Wilkinson is set to miss Sunday's Guinness Premiership clash with Wasps, the Powergen Cup tie against Leeds and back-to-back European Challenge Cup matches against Italian side L'Aquila.
Wilkinson has suffered a catalogue of unconnected injuries since dropping the goal which won England the World Cup two years ago - the last time he pulled on the red rose.
After recovering from an operation to correct a serious neck problem, Wilkinson suffered a haematoma in his arm and then two knee ligament injuries.
He recovered to make the British & Irish Lions tour but was then admitted to hospital with an inflamed appendix, which was subsequently removed, during Newcastle's pre-season tour of Japan.
Newcastle and England have been careful to manage his return to fitness carefully.
England boss Andy Robinson decided against selecting Wilkinson for the autumn Test programme so he could put a run of games together leading into the Six Nations.
Wilkinson's first two appearances of the season were off the bench but he has started Newcastle's last four games.
"It's yet another unfortunate blow to have Jonny out again with injury, but there's no point dwelling on it, you just have to deal with what's thrown at you," said Andrew.
"We're lucky in one regard at this club to have a number of quality players to cover that area, with Toby Flood starting there for us against Wasps on Sunday, and having a full international in Dave Walder as back-up on the bench."