They applied for entry into the Ryman League but they have not been allocated a place for next season.
Grays, who are now without a division as they have not applied to join the Essex Senior League, plan to appeal.
When it released the divisional set-up for the non-league game yesterday, the Football Association said a number of outstanding issues still needed to be resolved and the listings may be subject to change.
Grays were not accepted into the Ryman League because they had not submitted the relevant paperwork in time or clarified which ground they would be playing at next season.
Athletic owner Andy Swallow disputes that, saying he completed the application before the deadline and made the relevant parties aware of their plans to ground-share with East Thurrock United.
The 2005 Trophy winners finished 23rd in the Blue Square Premier this season, with just 26 points from 44 games.