The judge found that under the mother's care the boy would lose any relationship with his father and be "further harmed by exposure to the mother's continued anxiety and distress", court documents show.
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But before they left, the mother appealed against the decision - only abandoning it days before her appeal was to be heard.
She then raised safety concerns with the court about the boy travelling overseas because of Covid-19, preventing the pair from leaving New Zealand before another hearing.
Earlier this month, Judge Timothy Druce heard those concerns and accepted medical advice that the health risk to the boy was on par to him getting bitten by a shark or a volcanic eruption in New Zealand. He granted the father permission to leave with the son as soon as possible.
The ruling marked the end of a three-year legal battle that started when the mother breached a court joint parenting order in 2017 and failed to return the boy back to his birth country during a visit to New Zealand.
The father told the Herald he was relieved to be able to finally resume his life again after being in limbo for almost three years.
He had previously expressed frustration with the New Zealand Family Court's slow process and what he saw as its refusal to stand by a court joint parenting order agreed by the parents and lodged in three countries including New Zealand.
But the mother, who agreed to speak to the Herald for the first time this week, said she was heartbroken at their swift departure. She does not know when she will next see her son and worries for both his physical and mental wellbeing in the countries he is going to.
She also questioned why it was okay for the boy to be "ripped out" of the country he had lived in for three years, removed from his school and friends without even being allowed to say goodbye to his mum.
The mother said she believed the Family Court system was broken and had not looked after the best interests of her child.
"How is it okay for a child to be removed from New Zealand during Covid when every warning by the Ministry of Foreign Affairs says don't travel? How is that okay - how does that give the judge the right to say, 'Off you go?'"
She described the whole court process as toxic and claimed that while the November judgment raised concerns the boy would lose any relationship with his father if she had custody, the ruling meant he would instead lose his relationship with her.
The boy speaks to his mother two times a week as agreed in the court order. She claimed he was not in a good place last time they spoke. "He's breaking down."
However, the father said the boy was happy and excited to be returning to his birth country. They had been waiting to leave since the father was granted custody in November.
While the father had also been frustrated by the New Zealand court system, a positive was all the friends he had made and support they had given him both emotionally and financially because he was unable to work while on a visitor's visa, he said.
He was also grateful to his legal team who stuck with him over the three years and hoped the case would set a precedent for other parents in non-Hague convention countries or trying to travel during the coronavirus pandemic.
