Replacement maritime crew are seamen who are flown into a country to take over from those who have been on the job for a long period of time.
These workers are often only in New Zealand for a short period of time.
Even if a replacement worker is going straight from a plane to their ship, the new rules require them to be tested.
"The benefit of doing that is that if they do subsequently test positive, we will be able to do a contract tracing exercise for the very limited number of people they may have come into contact within New Zealand."
The Government will be covering the costs of the tests but Hipkins said it would not cover "huge numbers" of people.
In addition to this, crew leaving the country will also receive a test – this, Hipkins, will provide "end-to-end protection in this area".
"Our current border requirements have served us well, with recent cases quickly detected and contained – but there is no room for complacency," he said.
He said the Government recognises mandatory testing may present some challenges for the maritime sector.
But officials will continue to work with key stakeholders to ensure these new measures do not disrupt supply chains or put undue pressure on our managed isolation facilities.
"These changes balance the need to keep Covid-19 out at the border, while at the same time protecting the supply chain in order to ensure the flow of import and export goods to and from New Zealand."
Meanwhile, Hipkins genomic sequencing results from the testing of the Sofrana Civil workers in Australia revealed there is a match with the test results from the Covid-19 positive maritime workers in New Zealand.
"This means it's highly unlikely that there is another chain or transmission out there that we are unaware of."
