Fishing company Talley's has been accused of illegal trawling in a protected area of the Tasman Sea.
The Ministry for Primary Industries said the Nelson-based company and the master of one its vessels were each facing 14 charges, relating to breaches of the conditions of a high-seas fishing permit.
Greenpeace said the charges follow allegations that the vessel Amaltal Apollo carried out a series of bottom trawls, which could damage ocean corals and biodiversity.
It wants the boat placed on a draft global blacklist of illegal, unreported and unregulated fishing vessels.
Greenpeace executive director Russel Norman said they were now calling on the government to get tougher on fishing companies.
The ministry said it was the first case of its kind involving a New Zealand vessel being considered for such a listing.
The case will have its first hearing in the Nelson District Court late next month.