A former high-ranking priest has appeared in court charged with $666,000 worth of fraud from Auckland University of Technology where he was head of the business innovation centre.

Jonathan Richard Kirkpatrick was charged with 82 counts of making false invoices in the names of Halsey Consulting, Business Custom Solutions and Eventure.

The total amount of frauds charged added to $665,984.

He was also charged with two counts relating to, while being an employee, making entries in AUT's accounting system, Epicor, to obtain benefit for himself as a servant Kirkpatrick was arrested this morning.

He resigned from his role as chief executive of AUT's business innovation centre after large sums of money were discovered missing from research and development funds last week.

The former dean of Dunedin's cathedral was bailed to live at his address and name suppression was not sought.

His lawyer, Russell Fairbrother, said pleas were expected to be entered today but he sought a two week remand to do so.

"Mr Kirkpatrick takes full responsibility for his actions,'' he said.

Kirkpatrick was bailed with conditions that he surrender his passport and not enter AUT.

AUT would not confirm how much money went missing but it was initially believed to be about $500,000.

In a statement issued to students, vice-chancellor Derek McCormack said: "AUT has discovered some apparent accounting discrepancies. An internal investigation by AUT was undertaken in relation to this matter when it was first discovered, and this has now been referred to the police.

"The discrepancies were discovered within AUT's business innovation centre accounts and involves one staff member, who has now resigned.

"There are no indications that anyone else is involved.

"The discrepancies relate to money in the research and development field, and is not derived from student fees. Nevertheless, AUT is largely a student and taxpayer-funded organisation and remains accountable to the highest accounting standards.

"While I cannot comment as to the details of the case, as this is now a police matter, I want to assure you that AUT will do everything in its legal powers to recover any loss.''

McCormack said an internal investigation was underway to review AUT processes.