Maritime NZ cleared the ship, the Rio de la Plata, for pilot boarding.
"The ship was also cleared to berth by the Medical Officer of Health as part of the normal 'free pratique' process."
And a Port of Tauranga pilot boarded the vessel about 5pm on Wednesday and brought the ship into the Tauranga Container Terminal, she said.
"About 9pm, Customs NZ unexpectedly shut down operations on the ship and the local Public Health Unit advised Port of Tauranga that our pilot and the stevedores unloading the ship should go home and isolate while awaiting further instructions."
The Public Health Unit had since advised the port operations could resume on the vessel and workers no longer needed to isolate.
"Everyone in contact with the ship has been wearing PPE and no one on board has any symptoms," she said.
She said the port's primary concern was for the workers and health of those on board the ship.
"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."
Maritime Union of New Zealand national secretary Craig Harrison said the incident aboard the Rio de la Plata did not directly affect Maritime Union members.
He said it was a reminder that strict processes at ports were essential to protect New Zealand from exposure.
Harrison said there had been some confusion about the status of the vessel and its crew, and communication may have to be improved, but any false alarms were preferable to exposure to Covid-19.
Maritime Union wanted to see more proactive measures including public health staff visiting ports and having conversations with workers about the importance of vaccination, he said.
