National's Covid-19 spokesman Chris Bishop said the MIQ system has been in place since August last year and the Government has waited too long to try reclaim these overdue funds.
"We use debt collectors for student loans, for example, and at the end of the day this is money owed to taxpayers," he told ZB.
"I think the Government should have been using debt collectors far earlier than now."
He said handing over invoices to an external debt collector was a serious step with potentially serious impacts on someone's credit rating.
"So we want to be completely sure the invoices we send for debt collection are genuine unpaid debt so we have taken [the] time to make sure we get this right."
Meanwhile, Newstalk ZB can also reveal there was a significant spike in the number of MIQ invoices issued in June.
There were more than 6000 invoices sent out that month – that's 30 per cent of the overall 23,000 issued to date.
Milne said the reason for the increase was a system overhaul, which helped automate the programme.
"The fees regime was set up at pace, and at a time when it was unclear how long it would be needed."
He said the system has been heavily reliant on manual processing of data coming from various agencies that weren't always accurate or complete.
New funding has meant a new "streamlined" system making it quicker and more precise.
But Bishop said the fact that this was only happening now was problematic as it could mean millions of dollars worth of fees could have been missed.
"We need to know how many people they haven't invoiced to find out how much money the poor, long-suffering taxpayer missed out on because the Government hasn't been issuing invoices properly."