The 21-year-old has endured an unfortunate run with injuries in recent times, missing the whole of last season with ankle and knee problems.
Wilshere has impressed since returning to first-team action in October, but has now suffered an injury blow that will keep him out for three weeks.
The midfielder is out of Wednesday's Champion League clash at Bayern Munich as a result of the ankle injury, which Wenger revealed will also see him miss Arsenal's Premier League clash with Swansea and England's World Cup qualifying double-header against San Marino and Montenegro.
"Jack Wilshere is out," Wenger said. "He has an inflamed ankle, the other ankle to one he injured.
"He will be out for three weeks and will not be available for Munich, Swansea and not for England."
Wenger added: "Hopefully for the Premier League he will miss only one game. After there is an international break. We can slowly prepare him.
"I could see in the last couple of games he had started to dig deep.
"He has played 30 games. For us it is not welcome but maybe for him it is not bad that he has a little breather.
"It is more about prevention. The specialist decided he needed it. He has some bone bruising.
"The last time it deteriorated into a stress fracture. That's what we don't want to happen.
"We trust people who are specialists in this area. He was out for 17 months and we had to deal with it, we must be able to deal with it for two or three games."
Wilshere's injury absence is a major blow to hopes Arsenal have on Wednesday of turning around their Champions League last-16 tie with Bayern Munich.
The north Londoners head to Germany with the unenviable task of turning around a 3-1 deficit from the first leg.
As well as missing Arsenal's trip to Swansea in the Premier League on Saturday, Wilshere will be unavailable for Roy Hodgson's England side.
The midfielder made his senior debut against Hungary in August 2010, but will not be adding to his seven England caps this month due to his latest injury blow.
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