Port Taranaki will not allow the vessel with two Covid-19-positive mariners on board to dock.
Chief executive Guy Roper said he had not been told of Ministry of Health plans for the deep sea fishing vessel with all crew aboard to return to Port Taranaki.
Having the vessel return with known cases aboard puts staff and the community at a higher risk, he said.
Roper said throughout the pandemic the port had followed Ministry of Health protocols, including those for crew transfers.
"However we believe having the vessel return with known Covid-19 cases aboard is a completely different scenario."
As well as the safety aspect, the port needed to consider staff resourcing and customers, he said.
"We have a limited number of pilots, and the pilot on duty for the vessel's return would likely be required to self-isolate for a period and therefore be unavailable for routine cargo vessels.
"There is also no certainty about how long the fishing vessel would need to remain berthed without appropriate manning."
The mariners were in a group of nine sailors who arrived in Auckland on Monday without having to quarantine and were immediately driven to New Plymouth to board their deep sea fishing vessel.
All had provided negative pre-departure tests, but two returned positive results from swabs taken at at an airport testing site straight after they landed.
The mariners are isolating on the ship which is in international waters off the coast of Taranaki. The other seven have since returned negative Covid-19 tests.
The Ministry of Health regards the public health risk as low and said the mariners were not in any public places during their journey.
It has identified three contacts who are isolating, one of whom is a Port Taranaki worker who is fully vaccinated.
Director General of Health Dr Ashley Bloomfield told a media briefing this afternoon that the vessel was returning to Port Taranaki and the crew would be transferred to a managed isolation facility.