The Nigerian Football Federation (NFF) join Cameroon, who had initially filed a similar complaint to FIFA about the eligibility of some of the players who were born in Europe but switched nationalities to represent Congo internationally.
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The Super Eagles lost 4-3 on penalties to Congo DR in the final of the CAF Playoffs on Nov. 16, which meant the Congolese advanced to the FIFA intercontinental playoffs.
Congo DR have been drawn to play the winners of the semifinal between New Caledonia and Jamaica, with the victors in the final earning one of the final spots at next year's World Cup in the United States, Canada and Mexico.
But the NFF are now challenging DRC's use of several dual nationality players during the World Cup qualifying series, claiming they were ineligible on the basis of not being properly cleared to switch nationalities.
Reports have claimed that between six to nine players used by Congo DR during the qualifiers may have switched international allegiances, but may not have gone through the process of giving up their European passports in line with Congolese law before representing the country.
"The Congolese rules say you cannot have dual nationality," NFF general secretary Mohammed Sanusi told reporters on Tuesday. "There are so many of them that have European passports, some of them French passports, some of them Dutch passports. The rules are very clear. We cannot say anything now but we have submitted our protest to FIFA.
"There are players that got theirs in just three months. So there is to us, what is considered as a breach of the regulation. That is why took that decision."
While the Congolese Constitution does not recognize dual citizenship, FIFA's own regulations only require players to hold the passports of the representative country in order to be cleared to play for that country and it was on the basis of holding valid Congolese passports that FIFA cleared the players to play.
All the players involved hold Congolese passports, but Sanusi claims that FIFA were deceived into issuing those clearances
"The FIFA rules are different from DR Congo rules, that is why FIFA cleared them," he said. "FIFA Regulations say once you have the passport of your country, you are eligible. As far as we are concerned, they are eligible that is why they are cleared by FIFA.
"But our contention is that FIFA was deceived into clearing them because it is not the responsibility of FIFA to make sure that the regulations of Congo are abided by. FIFA goes by its own regulations, and it was on the basis of what was presented to FIFA that they cleared them. But we are saying that it was fraudulent."
FIFA has yet to respond to the complaint, but NFF officials told ESPN that the issue is being investigated by world football's governing body and a decision is expected before the intercontinental playoffs in March.
It is unclear if this appeal will be successful, but if it is, it would provide the Super Eagles a pathway back into World Cup qualifying, their second in the same series.
During the previous round, South Africa were sanctioned for fielding an ineligible player and docked three points, but Nigeria failed to take advantage and ultimately finished second in the group behind Bafana Bafana.
