Newtown School in Wellington is closing its main classroom block because it meets just 6% of the Building Code for earthquake resistance.
Parents were told of the decision at a meeting at the primary school on Thursday.
Older buildings are supposed to meet 35% of the Building Code.
About 150 children are affected by the closure of the main two storey block.
They will be taught in the school's hall, staffroom and a neighbouring school's hall for the next two days.
Plans for next week and beyond are still being made.
The school still has a single story classroom area in use, which houses its two new entrant classes in an open plan room.
There is also small classroom next to it that is unaffected.
Parents at the meeting say they are shocked by the news and are concerned their children have been in classrooms that are potentially unsafe.
The Ministry of Education says it will work with the school to house the students and no one has been in imminent danger.
President of the Secondary Principal's Association Patrick Walsh says many principals are worried students are being taught in an unsafe environment.
Mr Walsh says, as he understands it, the Ministry of Education is indicating there will be a 10 to 15 year timeline during which earthquake strengthening will gradually be brought up to a sufficient level.