Just half of contracted port workers deemed high risk have been vaccinated, despite a legal order in place.
Covid-19 Response Minister Chris Hipkins said on Wednesday about 61 per cent of all port workers were fully vaccinated and another 9 per cent had received one dose.
Not including the ports at Auckland, Wellington and Nelson, about 85 per cent of workers were fully vaccinated.
The main ongoing issues was around contractors, most of whom had less than half their staff vaccinated, Hipkins said.
"It is the contracted workers at the ports proving the most challenging and difficult to budge."
It comes after 11 of 21 crew on the Rio De La Plata container ship off Tauranga tested Covid positive, and 110 Port of Tauranga workers had to be tested.
Only a handful had been fully vaccinated, raising concerns the border message was not getting through.
Hipkins said the Tauranga low vaccination numbers were not an anomaly and reflected low rates particularly among contractors.
Hipkins named five port contracting companies and gave their current vaccination rates.
ISO Ltd had 200 workers vaccinated and 230 unvaccinated, C3 Ltd had 206 vaccinated and 201 unvaccinated, SSANZ Ltd had 157 vaccinated and 107 unvaccinated, Independent Stevedoring 63 vaccinated and 87 unvaccinated, and Wallace Investments 123 vaccinated and 60 unvaccinated.
A Ministry of Health spokesman told the Herald they did not know if they were fully vaccinated or had just received one dose.
It was also revealed vaccinations had now been opened up to all port workers, not just those on the frontline.
Port Company CEO Group chairman Charles Finny said he agreed the problem had been with port contracting companies.
"They have been subject to a legal order for several weeks now and their employers were aware it was coming ahead of that."
Misinformation was one issue, but another was that contracted port workers had until the end of September to have their first jab, meanwhile those in the public sector had until the end of August.
"So I think some people are leaving it late, but I think as the focus turns more to the border and people realise they need the jab to keep their jobs, they will come on board."
Finny said the group had met director general of health Dr Ashley Bloomfield on Tuesday to reiterate their call to expand vaccinations to all port workers, not only those on the frontline.
Bloomfield confirmed this had now occurred.
"It is great news, we have been calling for this for months," Finny said.
"Before, we had situations where vaccinated workers would come off working on ships and then have morning tea with colleagues who were unvaccinated. This should help boost those numbers."
The crew on the Rio De La Plata remained asymptomatic and the ship had now left New Zealand.
Genomic sequencing found the eight infected crew members had the Delta variant, and were linked to a Queensland pilot who had guided them along the Great Barrier Reef.
Meanwhile, mariners from the Mattina container ship currently in quarantine in Bluff also continue to recover from Covid-19.
As of Wednesday morning, 13 of the original 21 mariners remain on board the vessel.
Five crew members who returned negative Covid-19 test results, including the captain, have now completed 14 days' managed isolation. A sixth mariner, who has serological evidence of an historical Covid-19 infection, remains in managed isolation in Christchurch.
Of the 15 mariners who tested positive, three are considered by local public health officials to not yet meet the definition of having recovered.
Hipkins also announced on Wednesday Indonesia and Fiji have been designated as "very high risk" Covid locations and travel from the two countries to New Zealand will be limited.
Hipkins said escalating case numbers meant, as of 11.59pm (NZT) on August 15, travel to New Zealand from Indonesia and Fiji would be restricted to New Zealand citizens, their partners and children, and parents of dependent children who are New Zealand citizens (together with any children of those parents who are not New Zealand citizens).
Travellers from very high risk countries, including New Zealand residents, are required to spend 14 days outside of Indonesia before flying to New Zealand.
The "very high risk" category was introduced in April this year to reduce the risk of a large number of infected people flying to New Zealand.
Initially India, Brazil, Pakistan and Papua New Guinea were designated very high risk, and Fiji and Indonesia had now been added to the list.
"Currently there are more than 24,000 active cases of Covid-19 in Fiji, with the outbreak which began in April continuing to escalate," Hipkins said.
Hipkins said on Wednesday 2,293,000 vaccine doses had been administered as of midnight last night. Nearly 850,000 Kiwis are now fully vaccinated against Covid.
Hipkins also discussed the global situation and rising outbreaks from the highly-infectious Delta variant, suggesting a "swift and severe" response to any community cases here including heading straight to level 4 lockdown.
It comes as the Government prepares to respond to a major report on Thursday on New Zealand's path to reopening with the world.