The former world champion from Kentucky has undergone two operations on the problem in a season where he has collected a mere 29 points and finished in the top 10 just once.
Hayden initially went under the knife in June before then having a second procedure during the break in MotoGP's season.
The hope was that Hayden would be left pain-free for the remainder of the campaign after disappointing results so far this term.
However, the 32-year-old has been ruled out of the next two events in Indianapolis and Brno because of the recurring problem.
Provided he returns for the British Grand Prix at Silverstone, he will only be able to race at seven more events this season.
Leon Camier is to replace Hayden for the races in the US and the Czech Republic.