The Dairy Council for NI said survival was “questionable”.
It warned farmers would face a huge drop in the price paid for their milk, as dairies tried to face the extra costs of trade barriers.
It would see 10p per litre cut off the current base price for farmers, who are already producing at a loss at existing prices.
The council said if there was no-deal, companies could not process locally all the milk that would be produced in Northern Ireland.
It added they would not be able to cope with the tariffs and non-tariff barriers to trade.
“That would be a devastating situation for the Northern Ireland dairy industry, farming families, rural communities and the Northern Ireland economy,” said the council’s chief executive Dr Mike Johnston.
He said that would be a major threat to the jobs and livelihoods of more than 3,000 farm families across Northern Ireland.

In response, a government spokesperson said: “We are boosting preparations to ensure we are fully prepared to leave the EU on 31 October, whatever the circumstances.
“We are ready to intervene to provide support to some sectors in the unlikely event this is required and whatever the course of events, farmers will continue to receive the same funding for farm support until the end of this parliament.”
The Dairy Council for NI represents four companies which between them account for more than 90% of the 2.4bn litres of milk collected from Northern Ireland farms each year.
About 35% of the milk produced in Northern Ireland needs to be moved over the border for processing in the Republic of Ireland.
Dr Johnston said even if processing capacity locally was maximised, there would be a processing shortfall of 600m litres.
“If we don’t get a Brexit deal and cannot transport raw milk south, without significant delays and/or certification requirements, then our industry is facing a crisis of epic proportions,” he added.
“All processing sites in Northern Ireland will be full while there is no spare capacity to process that volume of milk in Great Britain.
“We have communicated these significant risks in the event of a no-deal to authorities in NI, the Republic and London but have not got any satisfactory outcome so far.”
Mervyn Gordon milks 160 cows near Garvagh.
He said government intervention would be needed to prevent farmers going out of business.
And he said some of the figures quoted by the Dairy Council were very worrying for farmers who were already losing money on every litre of milk they produced.