The News of the World claimed the 2006 opening could be delayed as consultants had been drafted in to recalculate computer data.
But the FA's Nick Barron said the £757m stadium will be completed "on time and on budget".
Barron said the roof - the biggest single span roof in the world - will be put in place in early 2005.
He told BBC News: "Despite what is in the papers today the FA has no concerns about the stadium.
The News of the World reported that Dutch consultants were brought in after fears over the initial calculations for the roof.
But Barron said this was because a sub-contractor, Hollandia, had been brought in recently and they wanted to re-calculate the specifications.
England’s Football Association (FA) has dismissed newspaper reports of structural problems with the roof of its new showpiece Wembley Stadium.
