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.
Lemina has made 12 appearances in Ligue 1 for leaders Marseille this season, starting six matches under coach Marcelo Bielsa, and it looks like he will be ready for club duty when the French league resumes next month rather than travelling south for the Cup of Nations (AFCON).
"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]."
Gabon have been grouped with hosts Equatorial Guinea, Burkina Faso and Congo in Group A with coach Costa selecting seven other France-based players on top of Lemina.
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.
Squad in full:
Goalkeepers: Didier Ovono (Ostende), Anthony Mfa Mezui (Metz), Stephane Bitseki (CF Mounana)
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)
Forwards: Pierre-Emerick Aubameyang (Borussia Dortmund), Malick Evouna (WAC Casablanca), Frederic Bulot (Charlton Athletic), Romaric Rogombe (AC Leopards), Johan Lengoualama (Difaa)
