La Roja had been upbeat on the teenager's chances of being fit for the game at Hampden Park but he has been unable to train all week because of a muscular problem
The Athletic Bilbao attacker suffered a tear in his right rectus femoris muscle but it had been thought that he would be available for the game in Glasgow.
However, team doctor Jorge Guillen has now confirmed that Muniain will not be available to Spain coach Luis Milla.
"He has been unable to train," the medic is quoted as saying by the Spanish Football Federation's (RFEF) official website. "As you saw, he could not do any intensive running yesterday [Tuesday].
"I think he needs a few days' training and I hope he will be ready for the game against Honduras."
Spain are scheduled to tackle the Central American nation at St James' Park in Newcastle on July 29 and will compete their group stage campaign against Morocco on August 1.