It is a move which has been welcomed by Otago principals.
Ministry of Education general manager Kim Shannon said non-core houses were those in areas where there was adequate residential accommodation, and were fully owned and managed by the ministry.
No schools in hard-to-staff areas - typically in rural areas - would be affected, she said.
"This was in response to the extraordinary costs imposed on the ministry by the Christchurch earthquake, earthquake strengthening of buildings nationally and weather-tightness remediation.
"Non-core houses are surplus to education requirements and have been - and are continuing to be - sold by the ministry as required by the Public Works Act 1981.
"The funds realised from the disposal of non-core houses will continue to be used to offset the cost of these national priority capital works."
Ms Shannon said there were also 173 core houses in Otago and Southland at present, which would not be sold.
"With a few exceptions, they have been transferred to the equitable ownership of boards of trustees. Boards are responsible for renting and maintaining core houses," she said.
Balclutha Primary School principal Paddy Ford and Wanaka Primary School principal Wendy Bamford said they were not concerned by the sale of non-core houses at their schools because they were outdated, and there were plenty of other rental properties for staff in the community.
Dr Bamford said Wanaka School had one non-core house.
"Wanaka is a big town - there is enough accommodation here to support the school, and it would be more modern and up to date than the school house."
Mr Ford agreed, saying he administered four non-core teacher flats in Balclutha, which were past their "use-by" date for professional working people.
"They tax the ministry's finances, and if selling non-core houses stops them from reducing ratios, that's all good," he said.
Otago Primary Principals' Association president Brent Caldwell said it was good to see the ministry was leaving core housing alone, because it was essential for small and rural schools.
"If I was a teacher from somewhere else, and I had to move to somewhere like Queenstown to teach, it would be nice to know there was a place with lower rent than what the open market could provide."
A list of Otago schools with non-core houses has been requested under the Official Information Act. A response is expected in 20 working days.
The disposal process is largely determined by the requirements of the Public Works Act 1981, which requires surplus property to be offered to other government departments, previous property owners and local iwi, before being placed on the open real estate market.
Ministry of Education properties can take between 16 and 38 months to sell, depending on disposal complexities such as subdivision, multiple titles (requiring amalgamation or separate offer-backs) and Maori land claims involving disputed or collective ownership, often requiring Maori Land Court decisions.