The Culture, Media and Sport Secretary, Chris Smith, has sent planners back to the drawing board to come up with a redesign that would allow the Olympics to be held in the new arena.
The FA executive director, David Davies, acknowledged the difficulties in satisfying all parties but said the new Wembley would continue to be the centre-piece of England's World Cup bid.
In a statement Davies said: "The FA welcomes the Secretary of State's reaffirmation that the new Wembley will provide the best venue in the world for the 2006 World Cup. Wembley will be the centrepiece of England's staging of that World Cup as Chris Smith confirmed today.
"Football, the national sport, has always recognised the difficulties of creating a stadium ideal for both our sport and a possible Olympic Games bid in the future. The concerns expressed today relate solely to the Olympic issue.
"As the Secretary of State has requested, both we and Wembley will of course continue to play a positive role in any further discussions with all those concerned. But there is worldwide recognition of the strength of England's bid for the World Cup 2006 and we are reassured nothing will be done to undermine that."
An independent sports architecture report commissioned by the Sports Minister, Kate Hoey, raised "serious doubts about the viability" of holding major athletics events in the new stadium. However, officials at Wembley National Stadium Ltd (WNSL) claim there are factual inaccuracies in the report and are confident the stadium can accommodate all three sports (football, athletics and rugby league).
At a press conference in London, the WNSL chief executive, Bob Stubbs, said: "We are pursuing the design as it stands. There are now a few technical questions we have to answer but we do not believe the design has any fundamental flaws. I don't think we are in breach of the Lottery agreement. The plans meet the requirements and we have not had any suggestion to the contrary."
Rod Sheard, one of the senior architects involved in the design, added it was too late to make major changes to the blueprint. "It is just not possible to change. We have been consistently working on this design for the last two years. There are now no black and white choices and that is understood by all concerned," he said.
The UK Athletics chief executive, David Moorcroft, applauded the decision to review the plans.
"The concept of a national stadium that can be good for both football and athletics, and potentially the Olympics, is inevitably going to be a difficult one and a challenge for the designers," he said.
"I think it's right that there is that review and that the review will be over quite quickly within 14 days."