Lemina declared on Twitter that "there has been no agreement between Gabon and me" despite Jorge Costa having earlier named the 21-year-old in his 23-man squad for the continental championships in Equatorial Guinea that start next month.
The midfielder was part of France's side that won the 2013 Under 20 World Cup and has previously declared his interest in catching the eye of senior coach Didier Deschamps rather than playing for the country of his birth.
"All that is being said are just rumors, I'm sorry but there has been no agreement between Gabon and me..." Lemina wrote on Twitter.
"I will not go to CAN [AFCON]."
Another Marseille midfielder - Alexander N'Doumbou, who has also started six Ligue 1 games this term - has been picked, as well as Bordeaux's Andre Biyogo Poko and Nice defender Lloyd Palun.
Borussia Dortmund striker Pierre-Emerick Aubameyang is the star of Costa's squad.
Defenders: Lloyd Palun (Nice), Yrondu Musavu King (Caen), Benjamin Ze Ondo (ES Setif), Bruno Ecuele Manga (Cardiff), Henri Junior Ndong (Auxerre), Aaron Appindangoye (CF Mounana), Johan Obiang (Chateauroux), Junior Randal Oto'o Zue (Sporting Braga)
Midfielders: Andre Biyogo Poko (Bordeaux), Didier Ibrahim Ndong (CS Sfaxien), Samson Mbingui (MC Alger), Mario Lemina (Marseille), Levy Madinda (Celta Vigo), Kanga Guelor (Rostov), Alexander N'Doumbou (Marseille)
