The Congo Football Federation tells BBC Sport they have filed a complaint to Fifa over Niger’s use of Mahamane Cisse in a 2014 World Cup qualifier.
Cisse, who has played for Mali at under-20 level, scored for Niger in their 2-2 draw with Congo on Saturday.
The draw denied Congo a place in Africa’s 2014 World Cup play-offs, withBurkina Faso advancing instead.
If Fifa rule in favour of Congo it would mean they would be awarded a 3-0 victory and so win Group E.
“We’re asking Fifa to look at whether the player (Cisse) was really qualified to play for Niger,” the Congo federation’s media spokesman Emmanuel Kaba told BBC Sport.
“The player was born in Mali, he’s lived for many years in Mali and we know that he played for the Mali under-20 team at the recent African championships in Algeria.
“We’re waiting for confirmation from Fifa.”
Only the group winners from the second round of African World Cup qualifying progressed to the deciding play-offs.
Under Fifa regulations players are allowed to swap national allegiances having played at youth level providing they have the approval of football’s world governing body.
Meanwhile the Tunisia Football Federation has also told BBC Sport they are looking into making a complaint to Fifa over whether Cape Verde’s Heldon Nhuck officially served a suspension.
Heldon picked up a caution in each of the opening two 2014 World Cup qualifiers and then did not play in the third game against Equatorial Guinea believing he had served his suspension.
However the match was later forfeited by Equatorial Guinea and so prompting Tunisia to investigate whether he was eligible to play against them on Saturday.
The striker went on to score for the Blue Sharks in their shock 2-0win that saw them qualify for the play-offs at the expense of Tunisia.