Federated Farmers fears there could be more seizures of phosphate bound for New Zealand unless political problems in north-west Africa can be resolved.
A 54,000-tonne shipment, which was being imported by fertiliser company Ballance Agri-Nutrients, was seized in South Africa en route from Morocco to New Zealand.
The phosphate was mined in Western Sahara - a former Spanish colony that Morocco claimed control of in the 1970s.
The national liberation group organisation Polisario regards itself as the legitimate ruler of Western Sahara and the shipment was detained after the group won a European Court ruling.
The future of the ship is expected to take weeks to resolve, and a Western Saharan campaigner said the political dispute could lead to more being halted.
Phosphate is essential for plant growth, and New Zealand imports around 400,000 tonnes of it each year.
Morocco and its Western Saharan territory produce 75 percent of total world exports.
Anders Crowfoot from Federated Farmers said New Zealand needed the phosphate and the price was likely to go up if the Western Saharan supply was taken offline.
"It's been an ongoing issue and it has been escalating ... [but] one would hope some of the politics could be worked out."
Vera Power of the Fertiliser Association said it was challenging to be caught up in the long-running political crisis and companies would have to look at contingencies.
These included importing phosphate from elsewhere, but other big producers - China, Russia and the US - have large internal demand for it.
Western Saharan independence campaigner Kamal Fadel said phosphate importers should be dealing with his people.
He said they owned the phosphate, not Morocco.
"We will continue to seek our rights everywhere anytime we have the opportunity," Mr Fadel said.
"We will use all the means available to us to protect our resources. These resources are non-renewable ... which we will need for the building of our country."