The Revenue Commissioners told the Irish Farmers Association (IFA) in recent weeks that there will have to be "checks" on cross-border movements once the UK leaves the EU, IFA President Joe Healy has claimed.
This is despite the December agreement between the UK and EU aimed at avoiding a hard Border and promising regulatory alignment, which Taoiseach Leo Varadkar described as "politically bullet proof" and "cast-iron".
Mr Healy said Revenue officials told him that "we can't have a third country without checks". Any potential checks would be of an electronic, administrative manner, rather than physical, he said.
"We met with Revenue in the past two weeks and they said 'Let's be real about this, we can't have a third country without checks'. They were very, very clear on it," Mr Healy told the UK House of Lords EU committee meeting in Dublin.
A spokeswoman for Revenue said the meeting took place on January 4 and also involved the Department of Agriculture. She said the reference to third countries related to current arrangements, rather than a post-Brexit scenario.
"It was made clear that the outcome of negotiations between the EU and the UK can not be predicted. As a result, no prediction could be made as to the practical implications for agri-trade and industry, post Brexit."
Mr Healy said politicians understand that they will not be "thanked in the long run if decisions that they take or agree to ends up back where none of us every wanted to return again, to a border".
"Revenue said, 'We don't want to go back to that, we want to try and avoid that', but [there was] no exact clarity as to what they have in mind, or where they could go, to ensure the checks are good and can stand up to scrutiny. But checks there will have to be," Mr Healy said.
Earlier in the hearing, Ibec boss Danny McCoy said the volume of growth in the Irish economy, driven in part by the accounting activities of multinationals, is masking the impact of Brexit for certain sectors.
Mr McCoy said businesses with low margins were already experiencing difficulties in the UK market, even though the economy is performing strongly.
"That dynamic is one of the backdrops to say that the momentum in the economy may be masking for some sectors the already perceived and real difficulties that Brexit has introduced both through uncertainty and exchange price movements," Mr McCoy said.
"Any fast-moving low-margins goods would already be experiencing difficulties in the UK market because it is the most dominant for a significant amount of our food.
"In terms of supply chain and retail, it's already being experienced on the ground.
"However, it is being masked by the sheer volume of growth that's occurring in the economy right now. Ireland is experiencing generational defying growth."
The Ibec Director General said the surge in growth experienced in the Irish economy as a result of globalisation and the on shoring of assets by multinationals is "the modern equivalent of an oil find".
"Ireland is a frontier economy for this new phenomenon of what is evocatively called capitalism without capital, where increasingly large corporations don't have physical assets," he said.