The injury, which is a hairline fracture to Rooney's left foot, is the third time the player has injured his feet wearing Nike boots since 2004. The manufacturer, Nike, has once again been under fire from the media, facing criticism that its boots do not provide players with adequate protection during games.
Rooney was taken off after just 45 minutes of the new season, when Reading FC defender Michael Duberry accidentally stood on his foot when challenging for the ball. He is now certain to miss England's crucial qualifying games for Euro 2008 against Israel and Russia.
Nike has been robustly criticised by former professionals and medical experts, who have argued that the "flimsy nature" of modern boots were making players more susceptible to foot breaks.
Professor Chris Moran, who oversaw Rooney's last foot injury at the 2006 World Cup in Germany, said: "There's no question that we're seeing more metatarsal injuries and that could be because boots are more flimsy.
"It can't be because players are tackling harder when the likes of Billy Bremner or Norman Hunter did when they were playing."
Ian Wright, the former England and Arsenal striker, added in his Sun column: "Rooney's boot looked like it didn't give him proper support. His foot seemed to be squashed far too easily.
"This latest spate of foot injuries must be linked to the lightness of the boot -- what else can it be?"
However, Nike has reacted strongly to the claims, stating Rooney's injury "had nothing to do" with him wearing Total 90 Laser boots, which were worn by 39 other Premier League players at the weekend.
In a statement, Nike said: "Wayne's injury was an impact injury which was sustained after a challenge from a defender. He has simply been unlucky. There's no evidence to link the boot with the injury, and both Nike and Wayne are positive about that."
While Rooney has remained silent on the issue, his club manager Sir Alex Ferguson has criticised Nike in the past over the player's previous foot injury, which occurred when the player was tackled by Chelsea's Paulo Ferreira while wearing Total 90 Supremacy boots.
Manchester United, which signed a 13-year sponsorship deal with Nike in 2000, has always denied that its boots are to blame for any player's foot injuries.
Rooney, who missed crucial matches in England's last European Championship and World Cup because of metatarsal injuries, joins a long list of England internationals that have damaged their feet wearing ultra lightweight boots -- including Gary Neville, Steven Gerrard, David Beckham, Ashley Cole, Michael Owen and Ledley King.