Before she applied to the Family Court to resolve the vaccine dispute, the man had supervised contact every second weekend with the two primary school-aged children.
Those visits have been on hold for the Family Court to decide whether one of the children, who is medically at-risk from Covid, should be vaccinated and whether the man's visits with both should be further suspended until that happens.
The court heard the child deemed most at risk from Covid has several health issues.
Medical specialists say he is prone to serious consequences from the disease and recommended both children be vaccinated.
In a recently-released decision, Judge Tony Greig said he was entitled to take note of the research adopted by the New Zealand Government and governments elsewhere that the Pfizer vaccine was safe for children.
The Care of Children Act 2004 required him to keep in mind the children's wishes, as much as their ages dictated, and make a decision in line with their welfare and best interests.
It was in the children's best interests to have the closest possible relationship that was safe for them to have with their father.
In this case, safety included ensuring the child who was particularly at risk from Covid was protected against it.
That risk would be significantly diminished if he was vaccinated and the science in support of that view was overwhelming, the judge said.
"Indeed, if (the child) was in the care of two parents who were refusing to vaccinate him, I would consider having him removed from their care until such time as he could be properly vaccinated," Judge Greig said.
He ordered the man's visits with his children be suspended until they were vaccinated to a level their GP was satisfied would provide maximum protection against Covid.
He rejected the man's contentions the visits could safely continue if he took precautions other than vaccination - by wearing a mask, sanitising his hands, and cancelling visits if he felt unwell. Contact could be outdoors or in a well-ventilated indoor area, the man said.
The judge noted those precautions did not include others such as having a rapid antigen test 24 hours ahead of contact and maintaining a two-metre distance from the children – all of which might be necessary.
Until the court was provided with more advice by the appointed supervisor and a medical professional, he was not willing to take the risk those precautions in the absence of vaccination would suffice, Judge Greig said.
He noted as an aside, the supervisor might not want to work around unvaccinated people.
The judge said he could review the case in future and "hopefully" reinstate the man's supervised contact.