A ship bound for New Zealand with 54,000 tonnes of phosphate may have to stay in South Africa for months while activists sue for compensation.
The NM Cherry Blossom was carrying one eighth of this country's annual phosphate needs, which were being imported by Ballance Agri-Nutrients.
But it was stopped at Port Elizabeth last month after claims the phosphate was illegally mined in Western Sahara.
A court in South Africa ruled overnight that the ship would have to stay there while two independence groups argued for either the cargo or financial compensation.
Ballance Agri-Nutrients chief executive Mark Wynne said the court's decision was very disappointing.
"The determination from the court means the vessel is likely to stay in South Africa for a very long time unless we discharge cargo or pay a bond. That's the next step."
Mr Wynne said his company had made contingency plans and there would be an adequate supply of phosphate for the coming spring.
Western Sahara was a Spanish colony that was taken over by Morocco in the 1970s.
Independence campaigners for the desert territory have been targeting phosphate shipments after the European Court ruled last year that it should not be considered part of Morocco for trade purposes.