"From the top of mind, Mr Hipkins, we have spent about $45 million additional on the system, remediating and getting it fit for purpose."
Mr Hughes said he would need to check that figure. Novopay had "cost us dearly", he said, but it was now performing adequately.
Asked about ongoing problems around calculating leave, he said the system could calculate staff leave, but its accuracy could not be guaranteed.
But he said that problem outdated Novopay and it was wrong to assume there was a "golden age" of past pay-roll systems.
Another exchange that enlivened opposition MPs came when the ministry was asked by NZ First education spokeswoman Tracey Martin why the struggling charter or "partnership" school Te Kura Hourua ki Whangaruru had not been shut down.
A series of articles in the Herald have exposed ongoing problems at the school, including management and student learning issues, and a falling roll.
The ministry was also asked why it continued to hold back an Education Review Office (ERO) report on the Whangaruru school - which in December officially changed its name to Te Pumanawa O Te Wairua.
Mr Hughes acknowledged current problems at the school around management and tracking student achievement.
He said at one point around 38 per cent of children enrolled at the school had not been attending school prior to their enrolment.
The ministry was working with the school to right its problems, but if that did not happen there were options available to the Government if issues could not be sorted.
Judith Collins, the National member for Papakura, asked if more could be done to assist families with disabled children, who were not getting a fair go from their local schools.
Ms Collins said a family had approached her because, "a particular school in my electorate is absolutely awful for kids who are disabled. And they make no bones about it - they don't want the kids there".
Mr Hughes said the ministry could help with arrangements could be made to send a child to a school out-of-zone, but its first preference was to work with the school in question to resolve any issues.
"Often there are some misunderstandings or they [the school] don't understand what support is available."