Trucking companies say a vaccine mandate at regional borders would be a problem because they are already struggling with a driver shortage and fragile supply chain.
The government is looking at making vaccination a requirement to cross regional boundaries for all but some travel.
Transporting forum chief executive Nick Leggett said the sector could not afford to take unvaccinated drivers off the road.
"We have a shortage of drivers and a shortage of people in the overall freight industry. We've got issues with ships being able to call at our ports," he said.
"We are compromised and a compulsory vaccine requirement at borders I think would cause significant disruption and slow our economy even further at a time when we can't afford it."
Anyone leaving Auckland for essential reasons must return a negative Covid-19 test in the seven days before they cross the border.
But the testing regime did not catch an unvaccinated person who later returned a positive result for the virus in Christchurch following a visit to Auckland - and now there are calls for vaccination to be a requirement for anyone leaving the region.
Leggett said drivers did not pose a great risk of transferring Covid-19 to other people.
"It's a solitary occupation for much of the time drivers are sitting in their cabs often not interacting and when they do interact they can have decent PPE and keep distanced," he said.
"We shouldn't run down a rabbit hole and compromise our supply chain potentially unless we really know what we are going to gain from a vaccine border mandate."
A recent survey of 300 transport operators showed 28 percent would not have enough truckies to run their business if a vaccine mandate was introduced, Leggett said.
First Union secretary Jared Abbott said unvaccinated drivers would probably lose their jobs, exacerbating the existing shortage.
"We have a real driver shortage in New Zealand and where we've seen these kind of mandates come in place on top of a driver shortage internationally it has had impacts on being able to transport freight which obviously we rely heavily on."
There was some vaccine hesitancy in the sector but the percentage of workers that was immunised was unknown, he said.
"I do know that there is a number of truck drivers that aren't comfortable getting vaccinations yet so I think there will be push back from those people but I can't speak on behalf of the companies that employ them."
There was growing unease about those locked out of jobs due to their vaccination status, Abbott said.
"It's easy to put a rule in to say you're locked out of the house but it's also the government's responsibility to think about what outside of the house looks like for people.
"It's a concern for us that we're seeing across a lot of industries people are becoming quite polarised on these issues and basically losing their jobs, losing their rights to participate in society."
Covid-19 Response Minister Chris Hipkins has confirmed a vaccine mandate for inter-regional travel is under discussion, including for domestic flights.
On the roads there were practical considerations such as keeping supply lines moving with minimal disruption, he said.
Director-General of Health Dr Ashley Bloomfield said people transporting goods were not to blame for spreading the disease in the current outbreak.
"It's almost entirely been within close contact settings, largely in the home but also in close contact within workplaces. So actually people in workplaces that are indoor are much more at risk than people who may have contact with drivers or others who are going about their work."
As for Auckland's border, Bloomfield said there had been a high level of compliance with the testing regime.
Otago University public health professor Nick Wilson said arrangements for the internal border around Auckland and the Waikato were "far too loose".
The requirement for a negative PCR test within seven days of crossing the border was "way too lax", he told Morning Report .
"There should be a requirement to be fully vaccinated and even to have a rapid antigen test at the border crossing point. This would help us avoid outbreaks in the rest of the country and give us more time to reach higher vaccination levels. It's really quite obvious."
"We're seeing problems with this border every few days and fortunately some of the problems have been dealt with - the cases in Wellington, Palmerston North and Blenheim, elimination has been reachieved - but we may fail with this current Christchurch situation."