An IFA statement read: "The IFA Appeals Board, after hearing lengthy and detailed submissions from Portadown, unanimously agreed to reject the club's appeal on the basis that the required documentation was not submitted on or before the deadline set by the Association.
"Therefore the original decision made by the IFA Executive Committee on Wednesday, 30 April 2008 remains valid."
A Portadown official said the club would not make any public response until the board of directors had met.
IFA president Raymond Kennedy stressed that the appeal had been heard by an independent board.
"They had an exhaustive, drawn-out meeting on Monday night and I have been told they had a fair hearing," he said.
"It is unfortunate for Portadown but the appeal board has made the decision and we have to stick by that.
"I feel sorry for Portadown but it is not the end of the world.
"They are a big club and they will recover and bounce back to where they belong."