Outside the court, Kirkpatrick said he had never intended to fight the charges.
When asked where the money was, his lawyer, Russell Fairbrother, said that would be clarified when Kirkpatrick appeared for sentencing.
Mr Fairbrother said the money was not overseas and had not been spent on vices. "He has not enriched himself."
He said his client co-operated with police as soon as the theft was discovered. "He wants to do everything he can to make amends."
Mr Fairbrother said he could not say more before his client was sentenced in October.
The Herald understands Kirkpatrick contacted police and offered to be interviewed when he learned his theft had been discovered.
Kirkpatrick is a former dean of St Paul's Cathedral in Dunedin and ex-partner of former Labour MP Tim Barnett.
After the Herald broke the news of the investigation, AUT moved quickly to file legal action against Kirkpatrick in the High Court at Auckland.
AUT spokeswoman Aimee Driscoll said the university was not commenting while the matter was still before the courts, but an email from vice-chancellor Derek McCormack was sent to all 26,000 students last month.
Professor McCormack said the "accounting discrepancies" were discovered in the Business Innovation Centre accounts and there were no indications that anyone else was involved.
"We are very disappointed to discover the discrepancies were by a trusted senior staff member, especially when money for research and development and tertiary education is scarce," said Professor McCormack.
"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."
Professor McCormack said AUT would do "everything in its legal powers to recover any loss", and a second investigation was under way to review financial processes.
Kirkpatrick has a long history in the Anglican Church and until recently was the priest in charge of St Albans in Balmoral.
But a church spokesman said Kirkpatrick no longer held any role of responsibility.
Before moving to Auckland, he was also the vicar of St Michael and All Angels in Christchurch.
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 he was thrown from a car after Mr Barnett fell asleep at the wheel and ran off the road in Dunedin.
