In his judgment, Justice Francis Cooke accepted the aviation security workers had proper arguments to be brought to court, and emphasised the importance of their ability to do so in an environment where those opposed to vaccination were liable to criticism.
He also acknowledged they had put themselves at risk as border workers for the benefit of the public, that they had now lost their jobs, and "should not be thought of as any less committed to the community than any other New Zealander".
However, the judge nevertheless rejected the three main arguments.
He said the requirement for border workers to be vaccinated fell within the minister's powers under the COVID-19 Public Health Response Act 2020 because they were measures that contributed, or were likely to contribute to preventing the risk of an outbreak, or the spread of the virus.
Justice Cooke, however, noted it was of some surprise such an important aspect of the response was implemented through an empowering provision which made no express reference at all to vaccination.
Significant measures of this kind would be better suited to legislation that squarely addressed the issues, he said, and his decision should not be interpreted as clearing a path for more extensive use of this power for other circumstances.
Justice Cooke also ruled that while the workers' fundamental right under the New Zealand Bill of Rights Act 1990 to refuse medical treatment had been limited, doing so was demonstrably justified.
The evidence, he said, showed the Pfizer vaccine was effective in reducing symptomatic infection, serious illness and death.
While the evidence was less certain on whether the vaccine limited transmission, it suggested it was likely and appropriate to take a precautionary approach given the seriousness of the harm caused by the global pandemic.
The judge also rejected the workers' argument the minister had failed to take into account relevant considerations, or made an irrational decision in implementing the order.
"I am satisfied that the vaccine is safe and effective, is significantly beneficial in preventing symptomatic infection of Covid-19 including the Delta variant, and that it significantly reduces serious illness, hospitalisation and death," Justice Cooke said.
"I also accept that it is likely to materially assist in preventing the risk of an outbreak or the spread of Covid-19 originating from border workers having contact with potentially infected persons from overseas."
The court reserved the question of costs.