Gap Connah's Quay have appealed against a point deduction imposed for fielding an ineligible player.
A Football Association of Wales panel deducted the club a point and fined them £250 for fielding Lee Davey as a substitute in a Welsh Premier match.
Davey had previously played for Colwyn Bay and Conwy Borough this season and participating for three teams in one season is not permitted.
Connah's Quay claim there was a problem with the FAW's registrations database.
"We apologise for any disruption that might occur to our colleagues as we take our right to appeal," the club said in a statement.
"We believe we are innocent of the charge brought against us by the FAW as both prosecution and jury.
"We are taking this fight forward and hope you will appreciate that, if we allow this injustice to proceed, we weaken all of the clubs.
"If the official Welsh FA registrations database is not to be trusted... then how are clubs to protect themselves in this situation?
"It could easily be you charged similarly next. If the official Welsh FA registrations database is not to be trusted and is dismissed by the FAW as just advisory, then how are clubs to protect themselves in this situation?
"We will avail of our right to appeal until no appeal process is left open to us. Unfortunately this may take some time."
Mark McGregor's side secured a place in the top six ahead of the Welsh Premier League's mid-season split with a 6-3 win at Bala Town.
Should their appeal fail then the Nomads would slip to seventh and into the lower half at the mid-season cut.
A statement on the FAW website confirmed that Welsh football's governing body had received notification of the club's intention to appeal.
"The FAW has just received notification (Monday) from Gap Connah's Quay that the club is appealing the one-point deduction imposed on them for fielding an ineligible player," read the statement.
"The next step will be for the FAW to appoint an Appeal Panel to be chaired by an independent person (not from the FAW) aided by senior FAW officials - none of whom were on the original Disciplinary Panel who decided to deduct the all-important point from Gap a week last Friday.
"The Disciplinary Department is fully aware of the importance of this situation and will conduct itself in its usual efficient manner."
No date has yet been set for the hearing.