This news medium understands that his Spanish La Liga side Villarreal have told the 19-year-old that he cannot play in both competitions.
The Under-20 World Cup ends in Poland on 15 June with the Nations Cup in Egypt starting six days later.
While reacting to the development, Super Eagles coach Gernot Rohr described it as a “dilemma.”
“It is a little dilemma that we must try to fix and hopefully there will be a good solution,” Rohr told BBC Sport.
“I understand when the club say it is impossible for him to play in the Afcon and youth World Cup.
“Chukwueze has good qualities and we already see why he plays at the top level in Spain.”
The winger has scored in La Liga, Europa League and Spanish Cup this season despite only earning promotion to the first team from the reserves.
On the international scene, he also made his senior debut for Nigeria against Uganda back in November 2018.
“He has an interesting ability which makes him a very important talent for any team he plays with,” Rohr added.
“I saw this quality when he played with us and the Olympic team, we must support Chukwueze and our other players too.”