Another 180 water fountains will be replaced and 26 water treatment systems are being installed to fix the problem, Jody Carr said.
Tests that began last fall found 147 of the province's 311 schools had water fountains with levels of lead and copper that exceeded Health Canada guidelines.
According to Health Canada, the maximum acceptable concentration of lead in drinking water is 10 micrograms per litre.
A spokeswoman for the Education Department said she did not have figures on the levels of lead that were found at the schools. Meg Cumby said the fountains were found to have either passed or failed the water tests, and those that failed were taken out of service until repairs were made.
Carr said the greatest problems were found in the Saint John area for several reasons.
"It can be the stagnation of the water because the water fountain isn't being used on a regular basis, it can be the age of the water fountain, or it could be the piping that leads to the water fountain," he said.
"It's really the contact that the water would have with any opportunity to be exposed to lead or copper."
Carr said more than $50,000 has been spent to provide bottled water in schools and another $320,000 has been set aside to replace water fountains.
He said it will be December before all the new water fountains and treatment systems are installed.
"We've also assured that we will not turn on a water fountain until it has the adequate standard for Health Canada," Carr said.
Carr said he was assured that the affected fountains would only present a health problem for someone drinking "two gallons a day for 50 years."
He said the department has changed the protocol for testing drinking water in the schools. In the past, the water was only tested where it entered a school, and the problems were only detected when testing began at each drinking fountain.
Carr said all fountains will be tested on an ongoing basis.
"It won't be all 2,000 fountains every year but it will be a rotation and a sampling and where there is remediation necessary we will respond to those," Carr said.