Ballance had been dealing with Moroccan supplier OCP for nearly 30 years and sourcing phosphate from that area for about 20 of those years, Mr Wynne told NZ Newswire.
The company was comfortable with the ethics and legality of the phosphate source after doing due diligence and consulting with the New Zealand government, he said.
"We take our guidance primarily from the UN Security Council."
He had visited the area last year and Ballance had taken into account the social impact as well as the likes of security of supply.
The NM Cherry blossom was one of about four annual shipments of phosphate rock which it blends to make fertiliser. It had been due in New Zealand at the end of the month.
Morocco is its main source of phosphate, but also sourced it from China, South Africa and Vietnam.
Contingency plans are underway to ensure farmers will still have fertiliser for spring, Mr Wynne said.
Morocco's government says it does not expect Polisario's legal challenge will succeed.
The hearing should test Polisario's use of a European court ruling last year that said Western Sahara should not be considered part of Morocco in European Union and Moroccan deals, Reuters reports.