There has been a "swift and intense" clean-up at Glenholme School after parts of the grounds were contaminated by raw sewage.
The school hall and field were flooded with raw sewage on Monday after stormwater drains on the surrounding streets overflowed.
Principal Nancy MacFarlane said they were alerted to the issue on Monday afternoon.
"The biggest lot of rain came down at 2pm and the toilets in the hall began overflowing. When the plumber came we realised the situation was a lot bigger than just a blockage."
Ms MacFarlane said the school had not faced this problem before, but she was confident the incident was a one-off.
"Considering how much rain came down in a short period of time, it was the perfect storm. But I think it was a one-time thing."
She said the affected areas were away from the classrooms. "There are no affected areas that will impact on learning. It's business as usual."
Ms MacFarlane said the clean-up had been "swift and intense".
"I appreciate that the Ministry of Education and the council have both been quick to respond."
But despite assurances there was no health risk to pupils, some parents chose to keep their children at home.
One parent, who wished to remain anonymous, said she was not happy with the situation.
"Quite a few of my friends are also keeping their children at home. We're told it's away from the classrooms and there was no health risk but it's the smell as well. It's not good for their brains.
"I don't know why the Ministry [of Education] hasn't closed the school. It ultimately comes down to whether you're willing to risk your child's safety or miss a few days of education."
She said she would assess the situation before deciding whether to send her children back to school today.
Ministry of Education deputy secretary of sector enablement and support Katrina Casey said the ministry was working closely with the school to ensure the health and safety of children and adults.
"The incident occurred at 2pm [Monday] and because the areas affected - the hall entrance including administration and bathroom areas and the north-east corner of the field - were easily able to be isolated, the school did not consider it necessary to close.
"The principal contacted us and we advised the school to seek specialist advice. We were assured that all affected areas had been isolated from children and that a plumber had attended to ensure no further leakage was possible.
"Activities usually held in the hall or on the field had been relocated to other areas within the school. All other parts of the school are not affected and are fully operational."
Ms Casey said the ministry's emergency response team would ensure all areas were free from contamination before being reoccupied.
Antimicrobial spray would be used on completion of the clean-up, she said.
"The health and safety of children and adults working in schools is of paramount concern for us so we will continue to monitor this situation until the all clear is given by the contractors.
"We expect the hall, apart from its office area, will be ready for use by [tomorrow] and the affected field area will be ready for use by early next week."
A Rotorua Lakes Council spokeswoman said the sewage overflow was a result of damage to the sewer main that was caused by heavy rain. She said workers found a power cable appeared to have been thrust through the pipe.
Council workers and contractors removed the overflow water by sucker truck, followed by two rounds of water blasting and disinfectant treatment on the field and around the hall.
She said there was no contamination risk, however the flood-affected areas of the sportsfield would be fenced off for about a week. Toi Te Ora - Public Health Service had been notified about the flooding.