Totara School, in North Otago, has been under statutory management for more than a year after three teachers left, the entire board resigned and many parents took their children out of the school.
She had been on mystery leave for more than six months, and a notice was sent to parents yesterday morning to inform them of her resignation.
Mr Hay said Mrs Spekreijse had decided to resign for personal reasons and she would not be returning to Totara School.
"We wish Sandra and her family all the best for the future and would like to thank her for her service to the school.
"We will now be commencing a recruitment process for a new permanent principal."
Mr Hay declined to answer questions as to why Mrs Spekreijse had been absent from the school and any further questions about her resignation.
The school was funded for 72 pupils last year. The school’s roll had dropped to 30 by the end of last year.
Relief principal Judy Elvidge has been acting principal since early February.
Under her guidance the school roll has risen, the ministry reporting a roll of 17 in March. Its roll now is 20.
Mrs Spekreijse had not been on the school grounds in her role as principal since October last year, following a "playground incident" in which a junior pupil was allegedly attacked by a senior pupil.
The investigation into the alleged playground incident had been completed, Mr Hay said.
He said the results of that process were confidential.
"The process has been completed, reviewed, internal processes have been implemented and other factors relating to this remain confidential," he said.
Mr Hay was appointed by the Education Ministry in March last year as limited statutory manager after issues arising at the school were brought to the ministry in January last year.
He has been commissioner at the school since June last year.
A Ministry of Education-led report delivered by Mr Hay last year stated issues at the school around relational trust, governance and management relationships, and communication breakdowns and pupils leaving risked the ongoing operation of the school.
Mr Hay said the rural primary school was "going very well" at present.
"The school is in very good heart, with dedicated staff, supportive parents and engaged students," he said.
Ministry of Education acting hautū (leader) Te Tai Runga (south) Andrea Williams said operational funding was calculated on the number of pupils enrolled at the school.
"If the roll numbers change, an annual adjustment is made to ensure that the school receives the correct funding entitlements for the year.
"Totara School’s roll-based entitlement staffing is 2.6 fulltime-equivalent employment," she said.
The school had a relief principal, two classroom teachers and two part-time teacher aides this term, and also employed an administrator and a part-time caretaker, Mr Hay said.
There was also an additional teacher aide in term 1 of the school year, he said.
Ms Williams said the ministry had been monitoring the intervention at Totara School closely.
The intervention would be reviewed this month, Ms Williams said, a little over one year since Mr Hay’s appointment as commissioner.
