The Pompey striker, along with Celestine Babayaro and Victor Agali, was sent home by the Nigeria FA for allegedly breaking a curfew - something which Aygbeni denies.
"Yakubu feels it is a great honour to play for his country," Portsmouth chief Peter Storrie told the club website.
"However, the way he was sent home and the stories given out by the Nigerian FA have left him extremely sad.
"He and the two other players were doing no more than enjoying a quiet coffee within the confines of the club headquarters.
"Because of the false stories which have come out he has been the centre of media attention for entirely wrong and unjustified reasons.
"The player would like the Nigeria fans to understand his position and says he loves his country will all his heart but has been placed in an impossible situation and can't contemplate returning."