The principal of Wairarapa College, Mike Schwass, has resigned for "personal reasons" amid a multimillion-dollar crisis at the school that sparked the sacking of trustees and the appointment of a commissioner.

Mr Schwass, who had led the district's largest secondary school for 12 years, announced his resignation in a statement sent on Wednesday afternoon to parents and caregivers and said he would step down at the close of the first school term on April 15.

Mr Schwass said he was stepping down "after consultation with John Carlyon, the commissioner of Wairarapa College". He said: "This decision has been made for personal reasons.

"It has been a privilege to be principal of this school and I have taken great pride, as we all should have, in the successes of our students in all areas of school life."

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Mr Carlyon, past principal of the school, took over as commissioner in the New Year after the board of trustees was sacked and limited statutory manager Michael Rondel was appointed at the school late last year.

Mr Carlyon revealed the school had slipped $1.86 million into the red and he was to present a recovery plan to the Ministry of Education asking that the debt be written off to avoid class cutbacks at the school.

Mr Carlyon said overstaffing had contributed to the financial straits in which the school was mired and five staff members were axed late last year.

The staff count was "now in line with the student roll," he earlier said, that last month sat at 1045 students.