One in five managed isolation bills has not been paid, according to official figures.
MIQ said it has sent out $170 million worth of invoices since the fees scheme started last year and $36m is overdue.
In August the amount of time returnees had to pay their bill was reduced from 90 to 30 days.
MIQ said that a debt collection agency has helped it recover about $1m of overdue fees.
But another 13,000 bills are yet to be sent out at all, due to invoicing issues.
National Party Covid-19 spokesperson Chris Bishop believes people should pay on arrival.
"There's still too long for people to pay. The government should really be chasing people who go through MIQ and have to pay.
"Everyone knows if you're liable to pay then you have to pay. It's not the way commercial hotels work, for example, and at the end of the day people are actually staying in a hotel."
Bishop said the current system is a mess.