The Nigerian Football federation says lesbians have not been banned from playing in the West Africa country.
It had been reported that football's world governing body Fifa had written to the NFF, seeking clarification over the situation.
NFF spokesman Ademola Olajire told BBC Sport: "Unfortunately, a section of the media has blown petty speculation out of proportion.
"The NFF never received any letter or query from Fifa."
The issue came to light when it was reported that Dilichukwu Onyedinma, the chair of the Nigeria Women Football League (NWFL), said lesbian players would no longer be eligible for the Nigeria women's national team and would "be sacked" from their club sides.
However, Olajire is adamant that is not the case.
"We have already circulated Onyedinma's speech at the NWFL's annual general assembly, clearly she never said anything of the nature that has been alleged," he said.
"The NWFL chairperson never made such sensitive comments and the NFF are not under any Fifa probe or query."
While contravening Fifa's anti-discrimination policies, the situation is made more complicated because homosexuality is illegal in Nigeria.
Currently, a Same-Sex Marriage (Prohibition) Bill that specifically outlaws same-sex unions is awaiting a signature from president Goodluck Jonathan to become law.
If that occurs, gatherings of homosexuals or any other support for gay clubs, organisations, unions - whether in secret or in public -will be banned, with same-sex couples facing up to 14 years in prison.
However, Olajire insists the football authorities will not be dragged into the homosexuality bill.
"We can only comment on issues concerning football in the land and nothing outside that," he said.
"The NFF operates on its own statues and that of Fifa, anything outside that is outside of our jurisdiction."
On the eve of the 2011 Women's World Cup in Germany, Eucharia Uche, then-Super Falcons coach admitted to purging the Nigerian team of all its lesbian players and argued that homosexuality is "spiritually and morally wrong".
Uche also commented that "the lesbians on our team were really a big problem."
Her reported comments drew a storm of protest from Gay Rights campaigners, and a number of groups wrote to Fifa president Sepp Blatter about the alleged ban.
But when pressed further in Germany, the former international performed a dramatic U-turn by denying quotes attributed to her.
The Super Falcons have won the Africa Women's Championship eight times, but exited the 2011 Women's World Cup at the group stage and did not qualify for London 2012.