The Government's old error-prone MIQ billing system has led to a failure to issue and collect more than $36 million in fees.

Newstalk ZB can reveal invoices for close to 14,400 people weren't issued due to "incomplete or inaccurate [MIQ] data" – this is despite these people having left managed isolation months ago.

There are also roughly 7,800 returnees who officials have not been able to figure out whether, or how much, they should be charged.

Written questions to Covid-19 Response Minister Chris Hipkins show there were problems with invoicing before the system was "streamlined" on March 24 this year.

It was around this date Hipkins revealed he was sending out debt collectors to track down money owed to the Government from returnees yet to pay their bill.  

National's Covid-19 Response spokesman Chris Bishop said it's "unbelievable" that so much money is missing.

"The Government can't run a functional invoicing system – it's just crazy and is another example of the incompetence at the heart of the Government."  

MIQ Joint Head Chris Bunny says he takes the recovery of the money owed for MIQ stays "very seriously".  

"Fundamentally, it is taxpayers' money and people should repay what they owe."

He says it's the Ministry's intention to invoice all those it's able to and that process will be complete early in the New Year.

"The new invoicing platform gives us the opportunity to go back and look at those older cases that we haven't been able to process because of a lack of data."

Bunny said the old system was heavily reliant on manual processing of data coming from various agencies that wasn't always accurate or complete.

As a result, he said invoices haven't been issued as quickly as he would have liked and there are some older cases the Ministry has not been able to assess due to incomplete data.

The $36 million in unsent invoices represents more than a fifth of the almost $153 million in invoices already issued to date.

But Bishop said it is unlikely officials will be able to recover all of that and much of it will have to be written off.

"That's money that's owed to taxpayers that will be written off and lost – that's on the Government."

He said it's clear that for a long time, the MIQ data was a mess.

"Officials were basically making it up week by week. It looks like they're trying to sort it out now – but what a mess it's been for the better part of 18 months."  

In mid-September, MBIE revealed it had issued more than 2000 MIQ invoices which were 90 days overdue – worth a collective $6.8 million.

At the time, Government debt collectors had brought in just $172,000 of the $2.13 million they've been hired to chase.

That number is now $4.3 million – with collection agencies chasing 1327 invoices which are more than 90 days late.

Of the total invoices sent, 2,594 are now more than 90 days overdue worth $8.4 million.