The North London club, however, denied media reports the 20-year-old would be sidelined for the rest of the season.
"The injury is in a different area to his previous [ankle] surgery. It will be reassessed in around two weeks by our medical team and medical experts who have worked together throughout Jack's recovery," Arsenal said in a statement on Wednesday.
"This is a recognised complication of a complex rehabilitation process and, of critical importance, Jack's initial injury is recovering well."
Wilshere has not featured this campaign after sustaining a stress fracture of his ankle in a pre-season friendly.
Arsenal, in sixth place in the Premier League, visit struggling Bolton Wanderers later on Wednesday.
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