The ports of Auckland and Tauranga are now requiring all international crews to do 14 days in managed isolation, and want other ports to do the same.
The ports of Auckland and Tauranga took the step despite Health Minister Chris Hipkins saying on Wednesday this would mean some ships would not come to New Zealand.
Mr Hipkins told RNZ every crew member entering the country could soon be required to be tested for Covid 19 but he had yet to decide whether to put all shipping crews through managed isolation.
Crews who are flown into New Zealand are at present taken straight to the port to join their vessel if it is leaving port that day, after being collected by a vehicle with a driver in PPE gear.
A report on the Port Otago Facebook page refers to the stance taken by Ports of Auckland and Port of Tauranga over managed isolation.
The Government at present allows international crews transferring on to foreign vessels visiting New Zealand to come through Auckland International Airport and transit directly to ports without isolation or Covid testing.
"Auckland and Tauranga ports are used for crew transfers, as they are within five hours driving time of Auckland International Airport and comply with these Ministry of Health rules," the Facebook post said.
"We occasionally have a crew member that needs to join a ship at Port Chalmers or Dunedin Bulk Port.
"In all cases, they must complete 14 days managed isolation and pass the required Covid testing before entering our port," the Port Otago statement said.
