About 1600 border workers are still unvaccinated while the latest data suggests up to about 1000 workers - including about 160 workers in MIQ - are overdue for their Covid-19 tests.
Meanwhile 77 per cent of Air NZ frontline staff are fully vaccinated, but 20 per cent - or 800 workers - are yet to have a single vaccine dose.
The figures have been released as the Government signalled a reopening of the transtasman bubble to some states from Monday, while Wellington will return to alert level 1 from midnight tonight.
Last week Sir Brian Roche, who chairs an independent group offering advice to improve the Government's response, said it was "critical" to set up a vaccinated safety barrier at the border.
On Monday the Government announced it would expand the public health order that currently requires all MIQ workers and government border workers outside MIQ to be fully vaccinated in order to work at the frontline.
The order doesn't apply to non-government workers at the ports and airports, but Hipkins said it will soon be updated to "extend the mandatory requirement to a much bigger group of workers".
As at 9pm on June 22, 9494 out of 11,438 border workers were fully vaccinated, 343 had received one dose, and the remaining 14 per cent - or 1601 workers - had no record of being vaccinated at all, according to the Ministry of Health.
Some of them may be exempt from vaccination or were yet to be matched to a vaccination record.
Hipkins said the weakness at the border was mainly at the ports, and the Government was working with employers to let them know if their workers were unvaccinated.
But while the Government had contact details for unvaccinated border workers, he couldn't say if any of them had been contacted to remind them of the importance of getting vaccinated.
"Some of those people who are in the system are only actually occasionally working in those areas of the port where there is higher risk," he said.
"We don't track and trace those people. We do have contact details for them, but we don't necessarily know when they're working at the border.
"We're working hard to make sure they know they can get a vaccination."
He said there was no weakness at MIQ facilities, and Air NZ was making "good progress" to vaccinate frontline staff.
Air New Zealand chief operational integrity and safety officer David Morgan said 77 per cent of its 4000 frontline workers in New Zealand were fully vaccinated - up from 76 per cent three weeks ago - while an additional 3 per cent had received one dose.
"It is important to note that the vaccine is not currently mandatory for our employees but is required for some duties (specifically crewing of MIQ flights from April 30, 2021)," Morgan said.
Brigadier Rose King said 96 per cent of 4166 MIQ workers - for the week ending June 20 - were fully vaccinated, while 105 workers had received one dose and 65 had no vaccinations recorded.
Anyone entering MIQ has to show proof of vaccination, but King said two workers who were yet to receive their second dose were wrongly granted entry last week.
"MIQ has reviewed these cases and reminded security, the employer and employee involved of the requirements."
The same percentage - 96 per cent - of MIQ workers were also being tested for Covid-19 within the legally required timeframe.
There were 44 MIQ workers still yet to be matched to their National Health Index number, and 407 MIQ workers who were overdue for their test.
Accounting for workers in the Waikato, where data has not been uploaded due to the cyber-attack, there were 161 MIQ workers overdue for their test.
Of those, 65 workers were less than four days overdue, 56 workers were four to 10 days overdue, 34 workers were more than 11 days overdue, and six workers had no test results at all.
Joint head of MIQ Megan Main said some of those shown as non-compliant may have in fact been tested on time, but data-matching issues such as duplicate profiles showed otherwise.
The Ministry of Health's latest data - for June 2 - showed there were about 930 non-MIQ border workers who were overdue for their Covid-19 test.
That suggests there could be up to 1000 workers at the border who were still being tested on time.
National Party Covid-19 response spokesman Chris Bishop said the threat of the highly infectious Delta variant emphasised the importance of having the border as water-tight as possible.
"I want to make sure every border worker is vaccinated as quickly as possible. I want to make sure our border testing regime does as good as it can get.
"Things can be a lot better than what they are."