Willis, the former England captain, claimed England had been scratching the ball to promote reverse-swing during their defeat to Sri Lanka at The Oval. The England coach, Ashley Giles, issued a firm denial at the time and now Bopara has also rubbished the allegation.
"We were doing well in that tournament and I felt it was unacceptable to make that sort of noise," Bopara told the London Evening Standard. "It was annoying, sad and depressing, especially in the middle of a global competition.
"When England are doing well, why does something negative have to come from it? Why not just get on the wave with England and enjoy it?"
Willis, as a pundit on Sky Sports, claimed that an unnamed England player was scratching the ball after it was changed during the group match defeat to Sri Lanka at The Oval - officially because it had gone out of shape. Willis said umpire Aleem Dar was "on England's case" after Dar and his colleague Billy Bowden had initiated a ball change that England appeared unhappy with.
Bopara was often responsible for looking after the condition of the ball, so an allegation of tampering could be regarded as a personal slight. But the ICC saw no reason in the umpire's report of the match for any investigation.
England found great success with reverse swing during their victory over Australia at Edgbaston - which George Bailey said he had been "very surprised" at - but struggled without any reverse movement against Sri Lanka. It was conventional swing that aided them in victories over New Zealand at Cardiff and in the semi-final against South Africa.
"We've learned over the last 12-18 months that we need to look after the white ball as well as we do the red ball," Bopara said. "We discussed as a team how we were going to shine it. You have to look after them to make them 'talk'.
"You want that seam to be standing up as long as possible; you want one side to be very smooth, which helps with lateral movement. If you can make the red ball swing, you should be able to do the same with the white one."