Africanfootball.com reports that a mandatory MRI screening carried out on 60 eligible players showed almost half were ineligible to play.
The existing first XI was far more badly hit, however, with only two players passing the MRI test - an astonishing blow for a squad which won the FIFA U17 World Cup last year for a record fifth time.
MRI tests have been used for several years to prevent age fraud in football, and are considered 99% accurate up to the age of 17.
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"It is a disaster,” a Nigerian official told the website.
"Virtually the first team the coaches have been working on have been disqualified. It’s a serious problem.”
The players who failed the tests have now left the training camp in Abuja, where they were staying ahead of Saturday's Cup of Nations U17 qualifying match against Niger.
"Several of the players were in tears and total shock when the final results came through," adds Samm Audu's report on Africanfootball.com.
"Among those who flung the age test was a star striker, who came through the national U15 team and has been outstanding in training leading up to Saturday’s AFCON qualifier.
"Another promising player disqualified only recently forced his way into the starting XI of coach Manu Garba’s team after a late call-up."
It's not the first time that age fraud has been discovered in the Nigerian youth system: back in 1989 the nation's youth teams were banned for two years for faking players' birth dates at the 1988 Olympics, for example.
It did not stop after that, however. In 2010 former Nigerian FA president Anthony Kojo Williams told the BBC: "We use over-age players for junior championships, I know that. Why not say it? It's the truth. We always cheat. It's a fact. When you cheat, you deprive the young stars that are supposed to play in these competitions their rights.
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