Schools were expected to upgrade classrooms to become "flexible learning spaces" - open plan learning areas of varying sizes to "encourage and support many different types of learning". Schools must pay for these upgrades using their five-year agreement.
Mr Gordon said high compliance costs had prohibited him from upgrading some buildings. He said adhering to Ministry standards for one building would cost $350,000 in earthquake strengthening, making the upgrade unaffordable.
"It's nothing that you would argue against but, if I'm going to touch a building, it has to be brought up to standard - and the cost expectations go up."
He said the nature of five-year agreements required long-term strategic planning.
"Sometimes you can't get to a particular building for 15 years, so we have to look at what remedial work can we do now to make that building safe, stable and usable for the next 15 years until we get to it. If you're ad hoc about it, you get into a lot of trouble."
In a written response, Ministry of Education spokesman Jerome Sheppard said the ministry expected to spend twice as much on school property this year as it did three years ago.
He said the ministry asked schools to prioritise property funding to make sure buildings were healthy and safe.
"If a school had health and safety issues, we would help them use their funding to address those. If they didn't have sufficient funds, we would step in immediately. The safety of the students and staff is our first concern."
Mr Sheppard said the Government had allocated $300 million over the next six years to assist schools with "complex property issues" which cannot be fixed from their regular budget.
The value of consents for education buildings rose 58 per cent in 2015, up $404 million to $1.1 billion. Tertiary buildings accounted for more than half of the increase.