Irish Cup finalists Crusaders were fined after the IFA ruled "inaccurate and misleading" information about the club's tax affairs was received ahead of a license being granted last year.
Details of the investigation into the Premiership club have emerged as Warrenpoint Town appeal a decision to refuse the club licenses to compete in the top two tiers of the Irish League.
The club has warned of the "catastrophic" effect on the club and the community if its appeal is denied following a hearing due to take place on Wednesday. Local politicians have lined up in support of the club.
While the IFA did not reveal details about why the licenses were denied, the club linked the decision to "an outstanding liability to HMRC of which the club was unaware".
It was "settled in full within a matter of days after it had been brought to the club’s attention by the IFA," Warrenpoint Town said. It is understood the bill was for approximately £14,000.
Clubs must either have fully paid all tax liabilities or have a time to pay agreement with the HMRC on March 31 every year, or face denial of license.
Crusaders faced scrutiny and a disciplinary hearing last year after the club told the IFA its tax bill was fully paid by the end of March.
This was both "inaccurate and misleading" as an investigation revealed it had not been fully paid, an IFA disciplinary committee found before fining the club £1,500.
Tommy Whiteside, the club's treasurer, insisted the situation was entirely different from that facing Warrenpoint as it related to conflicting documents among hundreds submitted as part of the licensing process.
The IFA was aware of a tax liability of around £160,000 reported in the club's accounts for the year ending December 2021. The club believed it was in a position to settle the bill before the end of March deadline but a large infusion of money did not come through in time, said Mr Whiteside.
A "time to pay agreement" with the HMRC was included in the submission documents, said Mr Whiteside. However, another document incorrectly stated the bill was paid in full.
In a statement, Warrenpoint Town said: "As a club we understand that the Licensing Committee have offered discretion to bigger and more established teams in the league, where the facts of the case were similar to our own.
"However, because we are a smaller regional club, it can’t help but feel like we are being treated differently. Our club currently relies on the efforts of our volunteers, and we don’t have the full-time support of employees dedicated to regulatory oversight like some of the bigger clubs will have."
The IFA would not confirm, deny or comment on the situation facing Crusaders last year.
