It raises the prospect of significant sanctions being brought against the Midlands club, including a potential points deduction.
The Rams drew 3-3 with Sheffield Wednesday on Saturday and only stayed up by one point ahead of Wycombe Wanderers, who are reportedly considering the prospect of legal action.
Reports suggest that if Derby are hit with a points penalty, it is unlikely to be imposed this season.
Last July, Sheffield Wednesday were docked 12 points after breaching FFP rules regarding the sale of Hillsborough, with the punishment enforced at the start the 2020-21 season.
An independent panel decided to halve their points deduction on appeal. The Owls finished three points below the Rams in the Championship table.
The Derby dispute centres on the size of the club's debts and using the sale of their Pride Park stadium to cover permitted losses, as well as anomalies in the ‘transfer values’ of players.
Charges were dismissed by the first independent disciplinary commission in August, 2020. But the EFL have now successfully appealed on the valuation of players issue.
An EFL statement read: "An Independent League Arbitration Panel has allowed the EFL’s appeal against the outcome of an independent Disciplinary Commission in respect of misconduct charges brought against Derby County.
"The panel concluded that the disciplinary commission was wrong to dismiss the league’s expert accountancy evidence, which demonstrated that the club’s policy regarding the amortisation of player registrations was contrary to standard accounting rules.
"More specifically, the panel determined that the club’s policy was not in accordance with accounting standard FRS102 because it failed to accurately reflect the manner in which the club takes the benefit of player registrations over the lifetime of a player’s contract.
"The original disciplinary commission had already concluded that the club did not adequately disclose in its financial statements the nature and or effect of its change in accounting policy, and there has been no appeal against that decision.
"The club and EFL will now have the opportunity to make submissions on the appropriate sanction arising out of those breaches.
"Despite media speculation, there is no definitive timescale for a determination on sanction, though the league will press for a decision as soon as reasonably possible and will provide a further update at the appropriate time.
"The EFL will be making no further comment on this matter at this time."
A Derby statement read: "The club accepts but is disappointed with the LAP’s (League Arbitration Panel's) conclusion on the one ground that the EFL succeeded on.
"The club and the EFL have agreed that the matter shall now be remitted back to the original DC (Disciplinary Commission) who can determine what, if any, consequences arise from the partial success of the EFL’s Amortisation charge, and the club is therefore currently unable to comment further."