Port workers who aren't Auckland or Tauranga based aren't considered high risk and don't have to undergo mandatory coronavirus testing.
Changes to the maritime border introduced at the weekend toughened requirements for testing.
Infringement offences were also introduced under the COVID-19 Act.
A Ministry of Health spokesperson says the mandatory testing focus was where there's a higher risk of infection.
The spokesperson told Newshub both Ports of Auckland and Tauranga are considered high risk because of the large volume of ships arriving from overseas.
"Mandatory fortnightly testing of higher risk workers at these ports will quickly detect any cases."
The spokesperson said voluntary testing was continuing at New Zealand's 17 other ports where ships were arriving overseas.
"Voluntary testing of maritime border workers has been regular and ongoing."
RNZ reported on Tuesday that only 1000 of the Ports of Auckland's 6000 workers would undergo the mandatory fortnightly testing.
"We don't think it's necessary to test people like truck drivers or people who don't go anywhere near a ship - there's no point in that, they don't come into contact with anyone from overseas," Ports of Auckland spokesperson Matt Ball told Morning Report.
