The Arsenal manager believes Stuart Pearce is putting Wilshere's long-term health at risk by selecting the 19-year-old, who has already played over 50 games for club and country this season.
Coming through: Wilshere is set to represent England at this summer's European U21 championships
'Jack Wilshere is in the red for a while now and this can be a risk for his health', Wenger said.
'He will respect the decision. He knows that he is nearly at the end of his energy level but he is keen to do well.
'Hehas played 50 games this year. To go to a tournament for me is a massive risk.
'I am happy if the Under 21s do well because I want England to do very well. I think it is not the right decision but willrespect (it) and let him go.'
Doubt: Carroll is uncertain whether his body will cope with the demands of U21 football this summer
Despite Wenger's opposition, Wilshere's selection is no surprise, with Pearce having included him in his provisional 40-man squad earlier this month.
Fellow senior internationalAndy Carroll was also included but there was doubt over whether the Liverpool striker would take his place in the final 23.
That was due to be announced on Thursday but the confirmed final squad will now be held back until Monday after the final round of Barclays Premier League matches, and the same day as the senior squad is revealed for the European Championship qualifier against Switzerland on June 4.
Carroll has told Pearce he is not sure his body will be able to cope with the demands of the European Under 21 Championship after playing for Fabio Capello's senior squad against Switzerland next month.
Jack's the lad: Wilshere has played 52 games for club and country this season
Starlet: The 19-year-old expressed his desire to play in the summer tournament
Carroll, who has made just nine appearances since December because of thigh and knee problems, believes his body would benefit more from proper rest this summer rather than thedemands of a tournament.
Reportssuggest the 22-year-old had expressed concern over his fitness after enduring an injury-hit second half of the season, and questioned whethertournament football could do him more harm than good ahead of the new campaign.
Also, like Wenger, Liverpool boss Kenny Dalglish has suggested he is not in favour of players being drafted backinto the Under 21 fold after graduating to the senior set-up.
Pearce has been adamant that including the best players at his disposal is crucial not only to England's chances this summer but also to boosting the country's hopes of success at future World Cups and European Championships.
One player who has confirmed he did not make the final 23 is Watford goalkeeper Scott Loach.
His omission may spark speculation Fabio Capello is preparing to make him a permanent part of the senior set-up following Ben Foster's decision to make himself unavailable for selection.
Loach, who was twice promoted last year following a series of withdrawals, wrote on Twitter yesterday: 'Didn't make final 23so no more 21s for me.
'Just an honour to have gained 14 caps for my country. Time to relax n have a few weeks off now.'
Both Wilshere and Carroll are expected to be named in the senior squad for the June 4 Euro 2012 qualifier against Switzerland at Wembley meaning they would miss the under-21s' pre-tournament training camp.
England's Under 21 Championship campaign begins on June 12 and they will play three games in eight days, and five in 15 days if they reach the final.
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Explore more:People: Jack Wilshere, Stuart Pearce, Andy Carroll, Fabio Capello, Kenny Dalglish, Ben Foster Places: Liverpool, United Kingdom, Switzerland