The 30-year-old, who has won 67 caps and played in all three Tests for the 2009 British and Irish Lions against South Africa, will have surgery under a local anaesthetic on Thursday.
Bayonne said on their official website Phillips will miss Saturday's Top 14 derby clash against Biarritz, with the club's medical staff predicting an initial two week lay-off.
Wales kick off their autumn Test series against Argentina on November 10, a schedule that also includes appointments with Samoa, New Zealand and Australia.
He would be an integral part of that campaign, in addition to Wales' RBS 6 Nations title defence later this season.
Phillips, meanwhile, is currently a clear favourite for the Lions Test number nine shirt against Australia next summer.
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