The warning from Pubs of Ulster, representing the retail licensed trade, comes following a meeting between police, publicans and local politicians in Irvinestown.
Following a landmark legal case the police have been checking premises to see if they are complying with the conditions of an Article 44 extension to their licence, allowing them to serve drink until 1am.
Those pubs that fail to comply, because they are not providing live entertainment or a substantial meal, cannot serve drink after 11pm.
Colin Neill, chief executive of Pubs of Ulster, fears that the enforcement of the licensing laws in this way will cause irreparable damage to the local economy.
Speaking after the meeting in Irvinestown, he said: "Pubs of Ulster are greatly concerned about the Article 44 issue in Fermanagh and whilst we understand and appreciate that the PSNI have the best intentions, we believe that the blanket objection (to the renewal of Article 44) is very heavy handed. We are concerned that these actions will damage forever an industry already struggling to survive.
"We are encouraged however by the constructive meeting held with the PSNI, local publicans and local MLAs. The meeting was very much an open forum, allowing over 60 concerned publicans to express the genuine fear they have for the future of their businesses. We hope that the PSNI now reflect on the concerns raised and continue to engage with Pubs of Ulster and the local trade to find a way forward that safeguards the future of pubs in the area," he added.
A number of local MLAs have also joined Pubs of Ulster in the call for a more appropriate approach to licensing laws, especially in relation to Article 44 applications, with a number also attending the meeting with the PSNI and local publicans.
Sinn Fein MLA Phil Flanagan said: "As someone who worked for many years in the hospitality sector in Fermanagh, I completely understand the frustrations of the local licensees at the approach being taken by the PSNI to this issue, particularly given the tough economic circumstances the pub industry is currently facing.
"There is a certain amount of flexibility that the PSNI need to exercise in this regard and that must begin with the removal of their objection to Article 44 applications and continuing to engage pro-actively with licensees in Fermanagh to rectify this situation," he said
"There is currently a review of licensing laws under way and it is imperative that local vintners have their say and that future laws meet the needs of a rural and tourist area like Fermanagh. As an MLA concerned about the future of the local pub industry, I will ensure that their voice is heard," he added.
Ulster Unionist MLA Tom Elliott said: "It is unfortunate that at this very difficult economic time many businesses within the service and hospitality sector could be forced out of business due to an inflexible approach from the authorities.
"I do not believe the current system is proving any more problematic than a change of implementation would, indeed it could be more practical for police to control and maintain. There is in general an excellent relationship between licence holders and the police. It is crucial for that to continue," he stated.
"The hospitality sector plays a vital role within Fermanagh's tourism and we need to support those within it as much as possible," said Mr. Elliott.
Pubs of Ulster said it would continue to engage with local pubs, as well as the PSNI and local MLAs, in order to find a way forward and ultimately ensure the future of the licensed trade in Fermanagh and throughout Northern Ireland.