Ms Hoey said the new pounds 475m stadium, the design for which was unveiled on Monday, was not representative of all sports but just national football. She said flaws in the plans could cost Britain the chance to stage future Olympic Games.
"If we want to bid for the 2012 Olympics, I don't think the country's hands should be tied behind its back from the very beginning by having the wrong kind of stadium," she said.
Ms Hoey is not the first to voice concerns about the new 90,000-seat Wembley stadium. It is intended as the centrepiece of England's bid for football's 2006 World Cup. Some estimates put the cost of changes needed to host a major athletics meeting at pounds 20m.
Ms Hoey, who succeeded Tony Banks as Sports minister four months ago, has ordered an independent report into the implications of the design.
The plans include provision for an athletics track but the capacity would then be reduced below the level required by the International Olympic Committee as a centrepiece to stage the Games.
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