Tauranga Mayor Stuart Crosby said he had been on the board of trustees at two schools so understood the challenges and how sensitive the issue was and was not surprised by the reaction.
The decision, made at last week's Long Term Plan deliberations, was not set in stone and the council hoped the Ministry of Education would help cover the cost. The decision would not be implemented until there had been sufficient consultation with schools, he said.
Otumoetai College principal Dave Randell said when the council made the same proposal in the early 2000s it was going to cost the school $10,000, although it was decided not to proceed.
It would cost the school a lot more now because the roll had grown to more than 2000 students - almost 500 more than when it was last proposed.
"It was a farcical exercise then and now it's happening again," he said.
"Last time we had to look at closing toilet blocks down."
Mr Randell said it was taking money out of education.
"It means I spend less in a classroom and more on toilets. They're trying to raise money for their own debt.
"It just seems ludicrous." Western Bay of Plenty Principals Association vice-president Matt Simeon, who is principal of Pillans Point School, said any increased costs for schools meant money had to be taken from elsewhere.
This could not come from set expenses, so had to come from variable costs such as professional development for staff and curriculum codes.
"It comes down to opportunities for kids becoming less and less."
Tauranga Boys' College principal Robert Mangan said increased rates meant more money coming out of operational funding.
"Financially, things are getting tight and I don't see the Ministry of Education giving us more money."
Otumoetai Intermediate principal Henk Popping said the increased rates would be another cost that schools had to absorb. "From our school's point of view, when we were paying rates on waste water it was quite expensive. It will just add another cost to the school that we will have to absorb."
Mr Crosby said the aim of the decision was to work with the city's schools to get more funding from the Ministry of Education for the increased operational costs.
"At the moment wastewater is heavily subsidised and we want to transfer this from ratepayer funding to the Ministry of Education."
"If it goes through, and it is still a big if, it is phased in over four years," he said.
If the ministry said no, Mr Crosby said the council would reassess. One of the problems with the scheme so far was principals had not been engaged with on the matter, he said.
"So they don't know where we are coming from, they have gone off their rocker with out understanding the principle behind it. It's not their fault, it's our fault."
Mr Crosby said the council should have engaged with schools earlier but the timing was not right.
The changes would not be introduced until next year as there had not been enough feedback from schools during the Long Term Plan process and time was needed for consultation.