The Secondary Principals' Association is concerned hundreds of schools may have earthquake-prone buildings.
The group's president Patrick Walsh says full survey work remains to be done but the cost of repairing buildings that are not up to standard could be tens of millions of dollars.
Mr Walsh has been contacted by principals who are upset the Education Ministry's repair proposals do not meet the recommended earthquake strength.
Some schools have been offered repair work to only 40% of the required strength for new buildings, despite the Department of Building and Housing advising all buildings should be at 67% of the code.
Mr Walsh says some schools are getting independent engineering reports in order to put more pressure on the Government.
He told Morning Report the Government needs to focus on strengthening earthquake prone school buildings, rather than repairing leaky buildings.
Mr Walsh says he thinks many of the old buildings will be discovered to have serious earthquake-proofing problems once the full survey is completed.
Society of Earthquake Engineers' executive officer Win Clark says anything less than 67% strength would mean people could probably not escape without being hurt in a moderate earthquake.
He says remedial work is a matter of priority.
The Education Minister has said in a statement that issues such as earthquake strengthening and leaky school buildings must take spending priority over the next few years.
An Education Ministry spokesperson says 40% is above the minimum legal requirement and if any school building was unsafe the ministry would act immediately.
