Salah played the full 90 minutes of Egypt's 3-1 defeat to Russia on Tuesday evening, the first time since injuring his shoulder in the Champions League final with Liverpool.
He scored the vital penalty which brought the 'Pharaohs' back into the game but ultimately lacked match and fitness sharpess due to his marred preparation.
Speaking after the result, Cuper argued: "When we talk about 100 per cent, we have to look at the medical side. I was told by the medical team he was fit.
"He could not prepare with us in the training sessions all the time, he had to train alone. I believe he was in good shape and optimal condition. If he did not get injured in the Champions League final then he would have had three weeks' extra training with us as a group.
"Salah is crucial, a vital player for the squad. He is a point of reference. He suffered an injury and we have been worried. We knew if he recovered in time it would be a good thing. The only thing I can be sad for is I would have liked to have seen him present at the training ground with the team."
"It's hard to say what would have happened if he was on top form but I always say that behind one or two brilliant players there has to be a team."