The 26-year-old striker was yesterday ruled out for up to two months after being fouled inside the penalty area early on in the Scottish Cup replay on the artificial pitch at Rugby Park, and though he scored the penalty himself, he immediately hobbled off.
After the extent of the damage was revealed, a thinly-veiled statement on the Rangers' website placed the blame firmly on Kilmarnock's pitch.
However, Clark has refuted this suggestion and called it a "cheap shot" at the Scottish Premier League strugglers.
The 43-year-old is quoted by BBC Sport as saying: "Serious knee injuries are happening on some of the best pitches in the world, so to link it just to the surface is just a cheap shot.
"I think it's a generalisation. I don't think it's come from one individual. Injuries are picked up both on grass and artificial pitches and that's the nature of the game."
Clark insisted that no member of the Rangers staff had voiced concern about the pitch before the game, and according to the Scottish Sun the surface was not mentioned as a possible contributing factor to Waghorn's injury when he spoke with Gers coach Mark Warburton after the game.
He told the Scottish Sun: "When I had a good conversation with Mark after the game... the pitch was never mentioned. The standard of it, the injury to Martyn Waghorn was never linked at all.
"In England, to get category 1 and 2 status in the academies you have to have these type of surfaces. If they were so bad, I don't think they would have elite players from all over the world training on them."
Despite losing Waghorn in the early stages, Rangers ultimately knocked Kilmarnock out of the cup with a 2-1 victory, with the striker's replacement Nicky Clark scoring an injury-time winner.