The Liverpool star scored a penalty for his nation in this evening's Group A clash against hosts Russia, but it was a disappointing evening as Egypt were beaten 3-1.
Salah missed the opening contest against Uruguay, which ended in a 1-0 defeat as he continued recovery from the shoulder injury that he suffered in Liverpool's Champions League final defeat to Real Madrid.
Following defeat to Russia, Egypt are on the brink of suffering elimination from the tournament at the group stage.
When asked about Salah's fitness after the match, Cuper told reporters: "When we talk about 100%, 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."
Egypt's final group match will be against Saudi Arabia.