Willis, England's second all-time leading wicket-taker in Tests, said that Umpire Aleem Dar was on England's case in the match against Sri Lanka: "He knows one England player, who I'm not going to name, is scratching the ball, and that's why the ball was changed.
"Have you ever heard of the batting side complaining about the shape of the ball, or the umpires saying 'we're going to change the ball because it's out of shape'?
"The bowling side change the ball because it's out of shape because they think it's gone soft. That's the reason, pure and simple. How naive does Alastair Cook think we are? The ball was changed because it was out of shape? He didn't want the ball changed, so why was it changed?"
Cook had countered the allegation, saying: "The ball was changed because it was out of shape. That was the umpire’s reasoning. The umpires make those decisions, so you have to accept them. Sometimes you don’t think they are the right decisions but there’s not much you can do about it.”
Giles, speaking for the first time since Willis claimed the ball was changed during Thursday's Champions Trophy loss to Sri Lanka because it had been tampered with, strongly denied the accusations. He was particularly unhappy they had surfaced ahead of Sunday's do-or-die Champions Trophy clash with New Zealand.
"We don't tamper with the ball and I hope we can talk about something else," Giles told a news conference.
"It is disappointing because we have a huge game, a quarter-final. Must win, and there are a lot of headlines about the wrong stuff. With the situation the other day, the ball was changed because it had gone out of shape. We asked the question, the captain asked that question to the umpires which he has a right to. The ball was changed, the rest is history."
Giles was far from pleased with what Willis had said, but refused to get drawn into a war of words.
"People have the right to say what they say, we can't stop them," he added. "It sounds boring, but we have to focus on what we want to do. The most important thing is winning cricket matches and not what Bob Willis says."
In reference to Willis' claim that a particular player was responsible, Giles said: "We play our cricket as hard as anyone else and the headlines are disappointing. There has even been mention of one of our players having a specific role. That player is an extremely good player and we'd like to let him concentrate on cricket."
Giles also defended his side's fielding methods. There have been suggestions England throw the ball in on the bounce in order to scuff it, but Giles said such moves depend on what ground his side are playing on. He added: "From the boundary you throw the ball in on the bounce because not everyone can throw it on the full. That's permitted."