Almost 6000 jobs have been lost in the agri-food sector since the Brexit vote in June 2016, according to Food Drink Ireland.
The IBEC group representing the food and drink industry says exports to the UK have fallen by €570m since then.
It comes as a new report warns that Brexit could cause as much damage as the economic crash.
The study, which will be discussed by Cabinet this week, says that depending on what type of Brexit emerges the economy could shrink by as much as 7% by 2030.
Kevin McPartland from Food Drink Ireland says the sector is facing an unprecedented challenge.
He said: "I don't think there is any way we can stop there being an impact from Brexit. Clearly, it's our largest trading partner, certainly for the agri-food sector, prepared consumer foods - 65% of all exports go to the UK.
"So anything that makes that more complicated is a problem, but we can manage that problem, we can mitigate the consequences, we can make sure that our relationship with the UK is as positive as possible.
"Yes, there is a threat, but we are managing the threat."