AUT has remained tight-lipped about the investigation, but vice-chancellor Derek McCormack sent an email to reassure the university's 26,000 students on Saturday.
He said the "accounting discrepancies" were discovered in the Business Innovation Centre accounts and there were no indications that anyone else is 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 Mr 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."
In the email, Mr 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.
Mr Kirkpatrick had worked at the university since 2002 and declined to comment at his Mt Roskill home when the news broke last week.
He has a long history in the Anglican Church and until recently had been the priest in charge of St Albans in Balmoral. However, a church spokesman said Mr Kirkpatrick no longer held any role of responsibility in the church.
Before moving to Auckland, Mr Kirkpatrick was the Dean of St Paul's Cathedral in Dunedin and the vicar of St Michael and All Angels, Christchurch.
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.
