The club's application to join next season's 12-team IFA Premiership was rejected by the executive committee - a ruling which, if upheld, will leave the Ports facing a minimum of two seasons outside of the domestic game's senior grade.
An IFA statement confirmed that "the application was not submitted by the stipulated deadline of four o'clock on Monday, March 31 2008, which was endorsed by the executive committee at its meeting on January 10 2008. The application has, therefore, not been included in the process".
Portadown officials have now handed the matter over to the club's legal team and a formal appeal was lodged with the IFA yesterday (Thursday).
Fans, left reeling by the news, have expressed concerns over the future of the club.
"I cannot believe how this was allowed to happen and do not understand the difficulty in meeting a deadline," said Ronnie McCoo, a committee member with Eden Reds Supporters' Club. "Every other club managed to get everything delivered on time.
"The thought of a club with Portadown's history and stature not involved in the IFA Premiership is practically unthinkable."
Danny Elliott, secretary of Shamrock Reds Supporters' Club, described the decision as "a disaster".
"We must be a laughing stock within football and there can be no excuse for being late," he said. "I hope the directors are planning to meet with supporters as soon as possible to explain the club's situation.
"Heads will have to roll as it is unbelievable that we missed the deadline."
It is understood that the final ranking of clubs will be announced next week and applications for the Premier Intermediate League must be submitted by no later than May 31.
"My personal opinion is that angry does not begin to describe how I feel about everything," said Leslie Cloughley, chairman of Richhill Reds Supporters' Club. "I am at a loss as to why such an important document was delivered late.
"If Portadown do have to spend time in the Intermediate League then it could prove disastrous for the various supporters' clubs.
"We depend on the parent club to keep interest going and numbers have already started to dip in recent times.
"If fans' groups start to lose money on away trips then that will affect the level of financial support to the parent club.
"I would also worry about what will happen to the players, plus the impact of legal costs at a time when we have invested so much into ground redevelopments."

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