Mercy Akide, Perpetua Nkwocha and Cynthia Uwak will miss Thursday's evening Caf Awards 2017 in Accra, Ghana.
African legends and past winners were invited by the Confederation of African Football for the event with the Nigerians left out.
US-based Akide made history when she became the first woman to win the African prize in 2001, while Sweden resident Nkwocha won a record four-time alongside two-time winner Uwak.
However, the African football body spokesman Junior Binyam has blamed logistic problems for the trio's absence from the Caf Awards Gala billed to be held at the Accra Convention Centre.
"For various reasons, I think Perpetua Nkwocha, Mercy Akide won't be able to make it," Binyam told Goal.
"I'm not involved with logistics aspects but as it was done for the male, most of the past female winners were invited.
"Yes, [it seems more of logistics problem] and basically because the time to prepare for the award was short. So, maybe in some cases as well others things were already planned by the time invitation were sent."
Meanwhile, reigning African queen Asisat Oshoala will hope for her third after she helped Chinese Women Premier League side Dalian Quanjian to a double, scoring 19 goals.