The Catholic Education Office says it needs extra funding from the Government to comply with proposed changes to earthquake strengthening rules.
Building and Housing Minister Nick Smith has proposed halving the period in which education and emergency buildings can be assessed and brought up to standard.
The Catholic Education Office is responsible for 340 schools throughout the country, and its chief executive, Pat Lynch, said it would cost about $120 million to bring them all up to scratch in that time.
"The Crown's not going to just say 'integrated schools, go away' when in fact we've been looking after ourselves pretty well, thank you very much," he said.
"But when something like this is dropped on you, well, that's what the partnership's about - to talk with one another and say, 'over a 10-year period, what can we do to help one another?'"
Mr Lynch said his office had already opened discussions with the Government about funding.