The IFA is warning that some people seem to be "sleepwalking into Brexit".
The Association's Regional Chairperson, Nigel Reneghan, says there is a horror story ahead for Ireland, if the UK leaves the single market and the customs union.
Mr Reneghan says Irish farmers will be hugely exposed if Britain negotiates solo trade deals outside the EU.
He said: "We are going to have to have more stringent checks on all produce coming from Northern Ireland into the Republic of Ireland, be that at Dublin Port or along the border.
"We can't have a situation developing where, that a country that is going to be effectively outside the EU market being able to take in produce and ship it in the back door into Northern Ireland, into the Republic of Ireland, and henceforth into France and other countries."