She said not only would farmers get lower returns, they may not get market access rights guaranteed by the World Trade Organisation.
Beef and Lamb chief executive Sam McIvor told RNZ prior to Brexit there was 228,000 tonnes of sheep meat access into the EU, including the UK, and 1300 tonnes of high-quality beef.
"What's happening with those quotas is that they now have roughly been split 50/50 between the UK and the EU so overnight we've had a significant reduction in the flexibility and the value that we can accrue from those quotas because we've lost the flexibility to put product into either the EU or the UK as customers demand it."
He said the export markets were massively important to New Zealand.
"What we'll see here is potentially reductions in export revenue to New Zealand. That affects farmers, it affects rural communities and that knocks on to every community in New Zealand."
McIvor said there was fear there would be future tariffs for importers like those in New Zealand.
Beef and Lamb are calling for flexibility in the quota.
He said the Government had done a great job advocating on the behalf of exporters and Beef and Lamb now expected the EU and UK to live up to their word that New Zealand would be no worse off under Brexit.
Trade and Export Growth Minister Damien O'Connor told RNZ he did not expect any more tariffs.
He said New Zealand was in trade negotiations with both the UK and EU.
"We have a great team of trade negotiators, we're upfront, we're honest, and we will do our very best to make sure our exporters get at least the equivalent deal that we've had and where even possible a better deal."
He said the Government was aware of the potential split in quotas and had been trying to assure the UK and EU the flexibility would assist their producers so that there was not oversupply at certain times of the year and undersupply at others.