The 19-year-old, who has burst onto the scene at Barcelona this season, was born in Spain, but had been eligible to represent Morocco through his father.
"Patriotism can't be bought or rented out. You can't reject citizenship," he told reporters.
"A while ago the Moroccan Football Federation contacted the player and his family with a view to him representing Morocco.
"If he plays one game for Spain then there is no turning back. His decision needs to be respected."
Munir is widely regarded as one of the best youngsters in European football.