The FAI have confirmed that Waterford have been denied entry to next season's Europa League.
This week, St Patrick's Athletic wrote to the FAI to question Waterford's eligibility for a UEFA license as club's trading company is less than three years old.
In order to compete in European competition, a club must be at least three years old.
Waterford FC's management company was only formed in late 2016.
Waterford qualified for the Europa League by finishing fourth in last season's SSE Airtricity Premier Division but the FAI say UEFA have denied their exemption request.
The FAI have not yet confirmed that St Pat's will take Waterford's place.
Waterford had requested a special dispensation from Uefa as technically the club has been in existence for less than three years.
However this has been rejected with the FAI releasing a statement from Uefa saying "Waterford FC’s exception request has been rejected on the non-fulfilment of the three-year rule as defined in the UEFA Club Licensing and Financial Fair Play Regulations.
It says Waterford FC may not apply for a licence for the UEFA Club Competitions for the season 2019/20.
On Wednesday night Waterford FC said they were not aware of any licence issues after St Patrick’s Athletic wrote to acting FAI chief executive Rea Walshe arguing that they should get the Airtricity League’s final place in the qualifying rounds of the Europa League because Waterford, are not eligible for a Uefa club licence.
In the letter, the club’s owner, Garrett Kelleher says St Patrick’s Athletic have taken advice from the European Club Association on the matter and that they believed Waterford were in breach of a couple of the criteria laid down for being granted the license they need to compete.