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The system was aimed at ensuring short-term returnees 'pay-to-stay', but the government admits it does not know how many of them have already gone back overseas.
A single person is liable to pay $3100 of the $6000 cost to accommodate them for a fortnight. A family of four's part-payment is $5000.
But of the first batch of 39 invoices sent in August, 13 were not paid 90 days later, with a total debt of $43,625.
Not all of the remaining 26 invoices had been paid - as some were granted a fee waiver after the date of the invoice. There are waivers for financial hardship and other special circumstances, such as compassionate reasons.
New Zealanders who are liable to pay include those staying for less than 90 days, and those who left New Zealand after 11 August this year and are returning home. Those who pay for their stay also include foreign nationals arriving as critical or maritime workers.
The country's 32 managed isolation and quarantine (MIQ) hotels are costing taxpayers more than $2 million a day, and are due to go over budget before the end of December.
"The first invoices became overdue on 26 November 2020," said an MIQ spokesperson.
"These invoices were for returnees who entered managed isolation on 11 August and left on 25 August.
"Once any invoices are overdue, they become a debt due to the Crown. MIQ sends a reminder 30 days before the due date to remind returnees about the invoice including details of how to pay, how to apply for an instalment plan, and what to do if the person considers they are not liable or are exempt.
"After the due date a further letter will be sent requesting payment. This letter will also contain details about how to apply for an instalment plan.
"If the person does not contact or pay, a decision will be made about the most appropriate course of action.
"Options include debt collection agency referral or court action. This decision will be made applying a consistent set of factors."
MIQ did not know how many of those who had been invoiced had since left the country after their visit, she added.
There are an average of 468 forecast daily vacancies in MIQ over the next fortnight, based on purchased MIQ vouchers. Yesterday, there were 5429 people in MIQ around the country out of the 6261 'operational capacity' spaces, which does not include emergency contingency places and quarantine rooms.