Western Sahara Campaign, a global advocacy group for Saharawi people, believed the people of Western Sahara, particularly those in refugee camps and liberated areas, did not benefit and did not consent to the trade of their natural resources.
The rock was extracted for Moroccan profit with no return offered to the people of Western Sahara, the Saharawis.
Thousands of displaced Saharawi live in camps near Tindouf in Algeria where they have been since the Moroccan invasion in 1975, Mike Barton from the New Zealand campaign said. But Ballance Agri-Nutrients chief executive Mark Wynne said he had taken the lead from the United Nations.
"The UN has a framework for managing trade in areas classified as non-self-governing.
"Ballance management and directors visit Western Sahara on a regular basis to evaluate compliance with both the UN framework and with our own legal and ethical criteria."
The phosphate rock made up about 70 per cent of Ballance's rock supply, Wynne said, and was ideal for New Zealand's soil conditions due to its high phosphorus and low cadmium levels.
The company used phosphate rock in the manufacture of superphosphate, which was made at the Mount Maunganui site and was required by farmers and growers.
In response to the protest, Wynne said he respected free speech and the right of everyone to protest.
"RMTU, in their request to hand the ship's captain a letter, stated that they didn't want to disrupt activity on the port. We facilitated a safe handing over of the letter and continued with the scheduled unloading of the vessel."
RMTU Bay of Plenty organiser Dasha Van Silfhout said the protest was the first of its kind at the Tauranga port but followed other protests around the country at Napier and Lyttelton ports this year.
"For us, it was a peaceful way of letting the crew know what they are carrying and what it is doing to the Saharawi people.
"Personally, as an indigenous person of New Zealand, it's the right thing to do and I know a lot of our members feel the same way."
A Port of Tauranga spokeswoman said the port supported port workers' rights to a peaceful and lawful protest. The IVS Windsor left the port on Wednesday, heading to Bluff.