New Zealand high school principals have been investigated to make sure they have not received unauthorised salary top-ups.

An Education Ministry audit on the salary top-ups, called concurrence payments, follows allegations Hamilton principal Martin Elliott misused money given to him when at Fraser High School.

Elliott resigned as principal late last year following the release of a report on the school's finances. It claimed he spent school money on his own properties but he maintained he'd done no wrong.

Though no charges have been laid in the case, the Herald on Sunday can reveal that some people connected to the Fraser High School saga have spoken with police.

The school's former executive officer, Jim Branton, who worked on the school's finances and who was one of the whistle-blowers, said he hoped the outcome of police inquiries would be made public soon.

"It has taken a toll on me because of the length of time it has taken to investigate," he said, adding he had encountered employment "challenges" since he resigned from Fraser.

Meanwhile, the Ministry of Education's group manager of resourcing, John Clark, confirmed the ministry had asked for concurrence payments to be checked in schools.

"This information has been supplied to the ministry and we are in the process of checking the information," he said.

The Herald on Sunday understands some principals were unhappy about the audit and felt it was an over-reaction.

"They discover a problem with one school and take a hammer to a nutshell...the auditors have been through the books with a fine tooth comb," said one source.

Concurrence payments are additional remuneration - up to about 15 per cent extra on top of salaries - that principals can get for duties performed beyond their normal responsibilities. This could include recruiting international students, running a school creche or special projects.

School boards must apply for clearance for the payments via the ministry. The cash comes from respective schools' operational funding.

Another source said one change being mooted following the audit included payments having to be authorised by the full school board in future, rather than by just the chair.

Elliott would not comment when contacted this week. He said he had put the saga behind him.

"I've got a new life now," he said. He now lives in the Bay of Plenty where he has been working on a "virtual school" for Te Runanga o Ngai Te Rangi Iwi Trust.

The trust's chief executive officer, Brian Dickson, said Elliott had not been charged over the Fraser High allegations and so he had no hesitation in giving him work.

"We will move on," Dickson said.

He said Elliott had been working with more than 40 schools in the district, tracking about 2000 students from the iwi and trying to work out how the trust could help them achieve higher school grades. He hoped programmes could run through the "virtual school" in time.

"We're hoping to get more grants to sustain it," he said.

He said Elliott had been doing "a good job" and came to him with the original idea. Elliott's wife Viv is from the iwi.