The UK and Europe are, in particular, New Zealand's biggest sheepmeat markets and Brexit could have a substantial negative impact on that sector, O'Brien said.
The New Zealand sheepmeat quota to the EU of around 228,000 tonnes represents over half of the sheepmeat export production and the UK takes half of that.
"The EU and UK markets have affluent and sophisticated consumers with Western tastes and they see lamb as a high-quality protein worthy of a premium price. Brexit could cause a significant disruption to supplying that market and if they can't get the product they'll go elsewhere," O'Brien said.
"Under Brexit the trade would face two years of uncertainty, if not longer, while the EU and UK negotiate as to who is going to take what part of the existing quotas."
Disruption of this trade could have widespread consequences, particularly for regional New Zealand, he said.
O'Brien said given the dairy downturn, New Zealand could not afford for its second largest export industry to have to deal with uncertain times in the UK and European markets.