"He's two months short of 12 and we explained that at the desk. I signed all the forms for unaccompanied minors and who was meeting him at the other end.
"I told them he went to intermediate and gave them the name of the school. They looked at his passport and then gave him his boarding pass," the grandfather said.
He took Jonathan through security, watched him walk down the air bridge and headed home, believing he was on the flight.
"Then we got a call from him to say he'd been thrown off the plane ... because he was underage. We had to come all the way back and found him standing there.
"We explained it all at the check-in desk. If you're going to have a dispute with a customer, the time to have that discussion is at check-in. You can't really issue a boarding pass and let them on the plane.
"You can't then change your mind and then have nobody at the airport to look after a little boy."
The man told the Herald he checked the conditions about unaccompanied minors on Jetstar's website before booking.
"We couldn't see anything in the small print when we booked so we assumed it was the same policy as Air New Zealand," he said.
"The real point I'm making is this is not how we do things in New Zealand. There's rules and whatever, but there's a way to do things and you can't do that to a child, then leave them alone."
The Jetstar website has information on children travelling alone to and from Australia, on intra-Asia flights and lists the school year children in Australia and New Zealand must be to fly alone. However, it does not have any information specific to New Zealand domestic flights.
Jetstar spokeswoman Andrea Wait said the airline required children in New Zealand who were not yet in Year 9 to travel with an accompanying passenger.
"The information is clearly available on our website at time of booking, and is reiterated in a reminder email prior to departure, and it is the passenger's responsibility to make sure they meet these requirements.
"This policy has been applied across our operations since commencing in 2004 and is because as a low fares airline, we are unable to assume responsibility for the supervision of children. This is common practice among low-fares airlines," she said.
But Ms Wait admitted the airline made a mistake with Jonathan.
"On this occasion, an isolated mistake was made at check-in when the agent assessed that the child met the criteria of the required year level at secondary school. However, it was subsequently determined prior to departure that this was not the case. It is common practice for various staff members to recheck passenger IDs throughout the boarding process where required.
"We regret [Jonathan] was checked in on this occasion. This was done in error."
The man was told he would be given a refund for Jonathan's ticket on his credit card. He paid another $100 to get the boy home on an Air New Zealand flight.