"It's not like test driving a car where you can drive a car for a week and take it back and pick up your old one.
"They've destroyed the old car effectively."
Mr Joyce also announced the Government will write-off small overpayments, totalling $440,000, because the cost of pursuing them exceeded the value of the overpayments.
The overpayments included 7,949 staff being accidentally being paid $6.05 on a public holiday plus other small overpayments which totalled up to $300,000.
Mr Vester said this was good news for his school - where his executive office had spent long hours chasing small errors made in the system.
Principal of Rotorua's John Paul College Patrick Walsh said Mr Joyce had made a careful decision but hoped it was the right one.
"One has to congratulate Steven Joyce - he hasn't made a rushed decision- it's been very carefully considered, we hope and pray it turns out to be the right one."
He said the Government couldn't afford to turn around and go to payroll provider Datacom.
The college were told by the ministry they had to pursue 10 former staff members who had worked for six months looking after a Japanese tour group who were overpaid by $26,000.
The money was taken from the school budget and one teachers was living in Australia and they had difficulty locating the person.
"Our executive officer had up to spend two weeks of his time tracking these teachers down and getting the money back."
Some schools had made arrangements with the Ministry to repay overpayments by $50 a fortnight.
President of the Secondary Principals Association Tom Parsons said the decision was the only logical progression.
"Novopay pre-Christmas, and Novopay now are two different beasts."
Mr Parson said his school had staff who had been overpaid by up to $6000.
"That's been resolved, and other cases are being resolved."
He welcomed smaller overpayments being written off.
He said Novopay was performing as good, if not better than Datacom.
Mr Joyce said the long-term future of Novopay is still under review after saying three out of four payrolls had shown an improvement in the number of mistakes.
Mr Joyce released figures showing the Government had spent $58.9 million on Novopay.
The Government was scheduled to spend $41.7m - an overspend of $17.2m.
There is still a backlog of 25,000 errors being fixed with Novopay and the system has 379 defects, 426 have been resolved and there are 197 new bugs.
What the Government has spent on Novopay:
* $29.4m start up costs and total for the implementation of Novopay.
* $13.8m operation of the Novopay service since go live to end of April.
* $8.2m cost to remediate Novopay including the Ministerial Inquiry, Deloitte technical review, programme management and reporting, provision of information.
*$1.5m Government funded remediation
* $6 million financial assistance to schools.
