Prime Minister Jacinda Ardern says MIQ bookings are protected from being swept up in an automated way by bots and scripts.
And she doesn't appear to be seeking a review of the system, instead simply asking people to use it fairly.
Her comments follow the ire of several frustrated travellers who have been unable to book any of the 2000 MIQ spots for November, which were swept up in a hurry.
Websites are now offering up to $2415 to use bots and scripts to quickly snap up an MIQ room, while one tech-savvy person is now voluntarily helping people book MIQ rooms with the help of a script that partially automates the process.
"People who are trying to go home to be with their father who has cancer, their mother with dementia. What am I going to do? I can't not help these people," the man, who doesn't want his name used, told RNZ.
Kiwi mother Jill Thompson said her two daughters in England have been wanting to come home "but it's just not going to happen this year at least".
"Ordinary Kiwis are seeing that there are 2000 spaces available, but when they try to book, there's nothing.
"Does the government know that the system is being used for someone to make a lot of money?"
But Ardern said protections were in place to give the MIQ booking system integrity.
"We've put in place processes to stop any automated way of being able to make that booking.
"We see no evidence that bots are able to actually make the bookings. You cannot automate the booking process. The individual still needs to go on and make the booking themselves, provide their details, and physically be a part of the booking process."
Asked if the system was being exploited, she said: "I would encourage people to just, you know, access that booking system in a way that's fair, but we have put in protections to try and stop people gaming it in any way."
There was now a "congested period" for MIQ places, she said.
"A few months ago, we had spaces. We keep imploring New Zealanders to keep an eye out for those times where we have reduced demand.
"We've bought in 150,000 [people via MIQ] - four times the amount per capita that Australia is now starting to bring in. But there are limits to what we're able to do."
Ardern said she believed taxpayers would understand picking up the tab for 1000 MIQ rooms in the next two weeks for people on mercy flights out of New South Wales - despite advice from the Ministry of Business, Innovation and Employment for them to pay for it themselves.
An MIQ spokesperson also said in April: "If there is a resurgence of Covid-19 and quarantine-free travellers to Australia are required to go into MIQ on their return to New Zealand, they will be required to pay for their stay."
But Ardern said the message from the Government had been clear from the beginning.
"When we announced the [transtasman bubble] pause, Cabinet had already taken the decision that if we were ever in a position where we, as a Government, required people who were in Australia to go into quarantine facilities, we wouldn't ask them to pay."
That was because there was a "do not travel" message for Kiwis for any other part of the world, she said, and if they did travel, they'd have to pay for MIQ when they returned.
"If there was a situation where we have circumstances like New South Wales, and we as a government decided that people needed to go into quarantine, travellers wouldn't have known that when they departed, nor could they reasonably have factored that necessarily in."
Ardern said the "flyer beware" warning was mainly about people being potentially stranded in Australia for a while, and that pre-departure testing and an MIQ stay on return may be required.
The cost of putting up travellers returning from NSW in MIQ was still unclear, she said - but there were 1000 rooms for the first two weeks, and the normal costs are $3100 for the first or only person in the room, plus $950 for each additional adult and $475 for each additional child sharing that room.