The mathematics block of Logan Park High School was vacated last July after the Ministry of Education found high levels of moisture and mould in wall cavities.
Pupils will return to the building this year following remediation work.
Ministry of Education acting head of property Simon Hatherill said concerns about weather-tightness were first raised in 2020.
It began investigating and then making repairs later that year.
Last year, the ministry was made aware of an issue with mould.
Testing began immediately and the ministry worked with the school to move classes to other buildings, he said.
It also put an air-monitoring system in place.
"The maths building has now been professionally deep-cleaned to remove the mould and tests show that it is safe to return to these classrooms."
The areas which were leaking had also been repaired.
Co-principal Kristan Mouat said the school acted before the test results were known, as a precautionary measure.
Parents and pupils were contacted about the issue, she said.
The buildings had since been fully remediated and retested for mould and moisture.
It was safe for use again and classes there would resume at the beginning of the school year.
A full school rebuild was planned, she said.
Mr Hatherill said the ministry was in the early master planning stage for a more holistic approach to the wider school.
The school was founded in 1974 and built on part of the reclaimed Lake Logan, which itself was originally a tidal inlet called Pelichet Bay.
The bay was partly reclaimed, creating the lake, but was later fully reclaimed to host the 1925 New Zealand and South Seas International Exhibition.
The buildings from the exhibition were demolished and the land converted to what are now the Logan Park playing fields.
The school was formed from King Edward Technical College, which split into Otago Polytechnic and Logan Park High School.
