Caucaunibuca, a star of the 2003 World Cup but not selected by his country for this year's showpiece, has failed to return to the relegated club for pre-season training.
Agen have now opened disciplinary proceedings against the player.
"Agen would like to state they have offered the Fijian player several opportunities to justify his absence since the return of training, but without any success," read a club statement.
"After three weeks of unjustified absence, the club has decided to start a judicial procedure against him and consider at present that he is no longer part of Agen's professional squad until the end of the season."
Caucaunibuca joined Agen in 2004, but did not score a try in 11 appearances for them last season.