The court found that if the mother was given full day-to-day care of the boy in New Zealand he was likely to lose any relationship with his father and be "further harmed by exposure to the mother's continued anxiety and distress".
The mother appealed the decision - but dropped it just before the hearing was due to go ahead this month.
But while the father was in the process of planning his trip home, she put in an application to the Family Court raising safety concerns about the boy travelling overseas during a global pandemic.
An urgent hearing has now been set to look at whether it is safe for the boy to travel overseas or whether further conditions need to be added.
But the father, who has been in New Zealand on a visitor visa since November 2018, said it was another slap in the face and more unnecessary legal delays.
Since the mother breached a joint custody arrangement made at a court in a non-Hague convention country and approved in two other countries, including New Zealand, and failed to return the boy by September 2017 - the father had spent thousands of dollars on legal fees.
Due to his visa conditions, the father has been unable to work since arriving in New Zealand in November 2018 in a bid to maintain a relationship with the boy and continue the legal process.
He fears the latest move is yet another delay tactic being paid for by taxpayers.
The mother has applied for legal aid to cover the latest costs, despite committing to pay for the boy to attend a private school, court documents show.
The father told the Herald he was extremely frustrated with the New Zealand court process and believed the countries he planned to travel to were safe and had fewer deaths from Covid-19 than New Zealand.
The father had initially planned to take the boy back to the country the father had lived in for 25 years. But due to the country's borders being closed had decided to go via his birth country and stay with the boy's grandparents until the borders reopened.
He ran out of money six months ago and the friends who had been supporting him had also been hit financially due to Covid-19. He feared they could be homeless before a decision was made about when they could leave.
"I have no medical coverage while I'm in New Zealand. How can anyone expect me to be here in a country during a crisis and looking after a young boy awarded to me by the New Zealand court... and literally I can hardly look after him."
He was extremely worried about how long they may have to wait for the safety hearing because based on his previous experience with the Family Court, he estimated it could take anywhere between two and 15 months for the next decision.
"The coronavirus could end and we could still be deliberating about coronavirus."
The boy's mother declined to comment, but told the Herald last year that both parents loved the boy very much and wanted the best for him.
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