Current Southampton manager Gordon Strachan is leaving the club at the end of the season after deciding to take a break from football, and speculation had linked Johnson with his job.
Johnson - who has previously managed the Latvian national team - has earned rave reviews after leading Yeovil to the Conference Championships and to the play-off positions in their inaugral season in the Football League, but insists that he has had no contact with the Saints.
He said: "It is always flattering but I'm under contract to Yeovil and Gordon Strachan is still at Southampton.
"I'm enjoying things at Yeovil and unless there is something official from Southampton there is nothing to discuss and no decision to make."