AUT successfully sought orders freezing his assets but the court file has been sealed from the public.
Aaron Lloyd, a partner at law firm Minter Ellison Rudd Watts, is acting on behalf of the university but declined to comment.
Mr Kirkpatrick, too, refused to comment when approached at his Mt Roskill home yesterday. "I'm not going to talk to you," he said.
Mr Kirkpatrick has a long history in the Anglican Church and has lately been the priest in charge of St Albans in Balmoral.
But Jayson Rhodes, spokesman for the Auckland diocese, told the Herald last night he had spoken to Bishop Ross Bay, who confirmed that Mr Kirkpatrick "no longer holds any role of responsibility in the church".
Before moving to Auckland, Mr Kirkpatrick worked in Dunedin and as vicar of St Michael and All Angels, Christchurch.
Yesterday, the university released a statement confirming his departure.
"As a consequence of AUT's investigations into the accounting discrepancies, Mr Jonathan Kirkpatrick has resigned. The matter is now under police investigation," it said.
AUT is making an urgent audit into the alleged discrepancies but will not reveal any details, including how long they remained undetected and how they were discovered.
Detective Senior Sergeant Hywel Jones, head of the Auckland financial crime squad, confirmed that a complaint had been laid with the police but declined to comment.
AUT sent an email to staff after the Herald revealed the inquiry yesterday.
It told them that no public comment was to be made and any inquiries should be directed to the vice-chancellor's office.
Mr Kirkpatrick had worked at the university since 2002. He has also been chairman of Incubators New Zealand since 2006.
Incubators New Zealand is a national association that aims to promote, foster and grow the incubation industry.
Mr Kirkpatrick has a high profile as a gay-rights advocate within the church. His relationship with Mr Barnett, the former Christchurch Central MP, lasted 18 years.
In August 1998, he broke his back when thrown from a car after Mr Barnett fell asleep at the wheel and ran off the road in Dunedin.
Mr Kirkpatrick has an MBA degree in commerce from Otago University and an honours degree in theology from the University of London.
He was a strong promoter of the AUT Business Innovation Centre and a lobbyist for business growth in New Zealand.
"Anybody starting a business based on innovation, especially technical innovation, needs to understand how hard it is," he was quoted in a business magazine.
"There are a million and one things that can go wrong, and the fragility of being a new business is ever-present."
