Crews from Balclutha and Kaitangata were called to the fire, in the school's boiler room, about 2.40am.
Workers were installing a new boiler system and fire investigator Murray Milne-Maresca said the fire was caused by sparks from grinding coming into contact with coal dust.
Firefighters brought the blaze under control after removing roofing iron, and remained on site this morning to tamp down any embers.
Principal Vicki Neave said firefighters' quick attention to the blaze had prevented it spreading to any classrooms.
She said parents and pupils should not be concerned, and the school would open for the new year as planned on January 30.
While the fire was not large, it did cause extensive damage to the school's boiler room.
Mr Milne-Maresca said it was important to take extra care when welding, grinding, working with hot tools, or undertaking any work with an open flame.
