Angela Walters has been acting principal since November 2018.
Naumann confirmed Shortcliffe's resignation to the Herald.
However, he couldn't confirm why Shortcliffe had been absent for so long or whether he had been on full pay the entire time.
"Unfortunately, employment law requires me to keep all information about the employment relationship confidential.
"I recognise that this will be frustrating for you but breaching confidentiality would not be appropriate or in the best interests of the school."
Naumann said the board would now begin searching for a new principal, but said the school had been functioning "extremely well" under the leadership of Walters and her team.
"Students are receiving a high-quality education and the school has made wonderful progress since its last ERO review in May 2018. There has also been significant roll growth in the past two years."
An ERO report published in March 2018, just before Shortcliffe went on leave, criticised the school's management. Among the raft of recommendations for improvement were that the principal needed to work collaboratively with senior leaders to implement a more inclusive approach to school development.
In a response to the Herald's inquiries last month about the school's management, Ministry of Education deputy secretary sector enablement and support Katrina Casey said it was inappropriate for the ministry to comment on an employment matter given the ministry was not the employer.
She referred any questions to limited statutory manager Naumann.
"As you will appreciate, any details of employment contracts are confidential. As all of the questions you raise are of this nature, I am unable to make any comment," he said.
Shortcliffe was appointed to the role in Hamilton in 2016 after eight years as the principal of Hastings Intermediate.
