The 20-player squad was also due to play against Italy and England.
The Uefa Under-16 Youth Development Tournament, which is organised by Europe’s football governing body, has been held since 2012.
It is intended to expose elite junior players to international football and ease their transition into senior levels of the sport.
Nigerian athletes and their supporters often complain about being denied visas by other countries, even when they say they have fulfilled all the visa requirements.
In February, Nigeria’s national football team pulled out of a planned friendly match against Argentina, which was to be held in the US, after the Nigerian players failed to secure visas on time.