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Six months after the fees scheme was introduced for the border hotels at least $23m worth of invoices have been sent out.
Returnees have three months to pay the fees, which are issued 'per room'.
By the end of January, an MIQ spokesperson said 7273 invoices had been issued.
Nearly 2000 of them - more than a quarter - had been paid, while 494 that were sent more than 90 days ago were overdue.
The fees are $3100 for one person plus $950 for each additional adult and $475 for each additional child - less than half of the total cost of each returnee's stay.
New Zealanders can apply for a fee waiver if they've been away from the country since for at least six months since at least 11 August 2020 and they're returning for at least three months.
Fee exemptions are also granted for people who are refugees, diplomats or consular staff, for those eligible on compassionate grounds, those returning after a medical air transfer or rescue at sea, or people being deported from Australia.
The government has accepted 81 percent of all applications, granting 3013 fee waivers.
An MIQ spokesperson said applications aren't processed if they're sent without evidence, "to ensure fairness and consistency".
People can apply for waivers before, during or after their MIQ stay.