Portsmouth are hoping to sign Liam Lawrence on an emergency loan from Stoke after a permanent deal between the two clubs collapsed.
Lawrence had been scheduled to join Portsmouth on a permanent transfer as part of the deal that saw Marc Wilson join the Potters with striker David Kitson heading in the opposite direction, but the Football League rejected the part of the deal involving the midfielder, claiming Pompey failed to submit the necessary paperwork before the 6pm deadline.
Pompey deny those claims but will now have to lodge a bid with the Football League to take the player on an emergency loan as the transfer window has now closed.
Lawrence, who is currently on international duty with Republic of Ireland, has not figured in any of Stoke's fixtures so far this season and is keen to seal the move to ensure that he is playing first-team football.
Stoke now hope to loan the 28-year-old to Portsmouth although the move will have to be ratified by the Football League, who will only authorise the deal if they are satisfied that the Championship side need him.
"We're disappointed that this transfer hasn't gone through," Stoke chief executive Tony Scholes said. "However, it is important that we work with Portsmouth, the player and the authorities to find an expedient solution as if it had gone through.
"The aim now is to ensure we arrive at the same point for both clubs and, most importantly, for the player who had made up his mind up to join Portsmouth.
"That will probably take the form of a loan move until the end of the year and then Liam would finalise his permanent move to Fratton Park in the January window. Clearly, we will co-operate with Portsmouth, the player and the authorities to arrive at a solution all parties desire."
Portsmouth later published a statement on their website admitting that they had been notified of their failure to deliver the correct paperwork in time.
The statement read: "Portsmouth Football Club have been notified by the Football League that the permanent transfer of Liam Lawrence from Stoke City has not been authorised because the necessary paperwork was not registered in time on transfer deadline day.
"Pompey are now working with Stoke and the League and are confident a solution will be found to overcome the administrative issue, meaning Lawrence will still join the club and be available for this weekend's fixture at home to Ipswich Town.''
A Portsmouth spokesman added: "It is obviously disappointing that we have had to adjust things but it is now just a paper exercise to make sure we end up in the same place as envisaged. Nothing changes in the sense that Liam is still fully committed to coming to Pompey.''