The Conference is yet to learn whether or not its clubs will be prevented from the year-round transfer of players.
The Football League has lost its battle with Fifa over continued dispensation from transfer windows and will fall in line with the Premiership next season.
And the Conference fears clubs could struggle if they are not allowed to alter their squads during the season.
Conference chief executive John Moules told BBC Sport: "It could affect us and we're waiting with baited breath."
He continued: "We need to see what the wording (from FIFA) is.
"We are waiting, with the FA, to see what the interpretation is and what affect it will have on football outside the Football League."