Altrincham have been charged by the Conference with an alleged breach of rules over fielding a player without international clearance.
James Robinson, 23, made 13 Conference appearances for Altrincham earlier this season after joining from Accrington.
It emerged he had apparently not received international clearance following a spell playing in Iceland.
Accrington have been charged by the FA but not the Conference as Robinson did not play a Conference game for them.
Former Crewe midfielder Robinson, who is now playing in Australia, has also been charged by the FA.
Altrincham could have points deducted if the case against them is proven.
Stanley say they were not aware that Robinson had played abroad and acted in good faith in handing him a trial.
Robinson played for the club's reserve side, but did not sign Conference forms and so Accrington will not face any sanctions from the Conference.
The FA commission which will hear Accrington's case have "all options open to them" but it seems likely that any penalty Stanley might receive would amount to no more than a fine.
He then joined Altrincham, scoring four times, before leaving to join Australian side Richmond Eagles in February.
With Altrincham just six points above the Conference's bottom-two, any possible points deduction could have a bearing on the relegation issue.
However, Altrincham also believe they acted in good faith in signing Robinson from another English club.
"I have been dealing with the FA over this matter for the last fortnight and I am comfortable with the outcome of those dealings," manager Graham Heathcote told Altrincham's website.
"The matter is also being considered by the Football Conference, who have been made aware of the FA's findings."
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