Eleven of 21 crew on the Rio De La Plata container ship off Tauranga have tested Covid positive.
Ministry of Health officials this morning said further testing would determine how many crew were active cases and how many were no longer infectious.
Ninety-four port workers, who spent time on the vessel, have been stood down until they returned a negative test. Testing for staff was being arranged at the port this morning.
The Port of Tauranga said in a statement it treats all vessels as if they have Covid-19 on board.
"All port workers who interacted with the ship followed the usual Covid-19 precautions, including physical distancing and wearing PPE," the statement said.
"Out of an abundance of caution, public health authorities have advised workers who boarded the ship to self-isolate and be tested for Covid-19 on Monday morning.
"Cargo loading and unloading at Tauranga Container Terminal will operate at reduced levels whilst we work through this situation.
"The health and safety of port workers, their families and the community are our top priority. We will continue to follow all advice and directions of public health authorities."
The Rio de la Plata was the subject of health authorities' attention earlier in the week after an Australian pilot on board two weeks ago tested positive for Covid-19.
The vessel was at Port of Tauranga from 6pm last Wednesday to 2pm on Saturday.
It comes after the Bay of Plenty Times reported on Thursday of port staff being forced to isolate after Customs NZ unexpectedly shut down operations on the ship.
However, the Public Health Unit later advised port operations could resume on the vessel and workers no longer needed to isolate.
A port spokeswoman told the Bay of Plenty Times the ship had been cleared by the Medical Officer of Health as part of normal protocol.
"This has been a very unsettling, stressful and frustrating situation for the workers involved and we will be working with government agencies to ensure this situation can be avoided in future."
The Singapore-flagged ship is linked to a Covid-positive Australian pilot who was on board the vessel in July in Queensland and who developed symptoms and tested positive for the Delta variant nine days after being on board.
The pilot was not linked to any other Queensland cases.
The ministry said Rio De La Plata had berthed at Botany Bay, New South Wales, after the pilot disembarked in Queensland.
The ship left Botany Bay on July 25 and berthed in Tauranga on August 4.
Public health staff took swabs from the crew as part of the requirements for entry to Napier, its next destination.