The Government's existing mandate requires only frontline workers at ports who work directly with international ships to be vaccinated.
More than 500 people are understood to work at Napier Port in varying capacities. Under the port's new mandate, all are now required to be jabbed whether they work closely with ships or not.
A maritime union - which has about 300 members at Napier Port - says the mandate will result in people losing their jobs.
Rail and Maritime Transport Union general secretary Wayne Butson said the vast majority of workers who access the port supported vaccinations, but there was a "handful" of workers that he knew of who did not want to get the jab.
He did not specify the exact number of workers refusing vaccination.
"The union's national policy is that we support vaccinations, and we support having vaccinated workers, particularly on front lines.
"There has been some fallout in Napier with some people who continue to be vaccine resistant, and they are all being dealt with between the local union branch and Port of Napier management."
He said it was much tougher to redeploy staff who did not want to be vaccinated into other roles under this latest policy, because it covered the entire port rather than just frontline staff.
"When the employer goes down the mandating path, of course, that just removes the alternative employment, or redeployment, option."
He said it was important that businesses follow proper risk assessments when making a decision to introduce mandatory vaccinations. He said a new Bill currently before Parliament would help provide "greater guidance and consistency".
The Government is currently fast-tracking legislation which includes a clearer process on how individual businesses can introduce their own vaccine mandates using a risk "assessment tool", as part of the Covid-19 Response (Vaccinations) Legislation Bill.
However, Napier Port chief executive Todd Dawson said that Bill would not have much impact on their plans whether it was passed or not.
"We are very close to having all of our Napier Port employees fully vaccinated," he said.
"We're working with other port users around our expectation that everyone coming on to Napier Port is vaccinated before the end of the year.
"Availability of the vaccine pass makes that process more straightforward now."
Labour's Napier MP Stuart Nash, who is also the Minister for Small Business, clarified the new Bill going through Parliament did not "override" steps already taken by businesses to legally introduce their own vaccine mandates, through existing health and safety guidelines.
"This new process won't override risk assessments that businesses have already done under the existing health and safety guidelines.
"Businesses can choose which one they use, and any assessments done to date remain valid," he said.
"Vaccine requirements in the workplace are a common tool many countries are using to stop the spread of Covid and to protect their workers and customers from the virus."
Testing
All Napier Port employees are now required to be tested for Covid every two days.
The port has invested in saliva PCR tests which return same day results.
"Napier Port has around 320 employees who will be tested every two days with same day results," a port statement read.
"With this rate of testing, there is a reasonable likelihood that Napier Port will identify cases which we will support and liaise with public health for verification."
The new testing requirements do not apply to port workers who are not directly employed by Napier Port.