This was one of 68 education centres around the country closed this week due to flooding, Ministry of Education statistics showed.
Napier Kindergarten association general manager Helen McNaughton said the closure was a "flow on effect" from the flooding across the Napier sewage system.
On Wednesday the council had asked residents to cut back on flushing their toilets, have shorter showers and washing cycles to take pressure off the waste water system, which often happens during heavy rain.
However the amount of water in the system meant the toilets at the Hurst Ave kindergarten were backlogged.
"We've got 40 children and some adults, who are teachers, [at the kindergarten]," Ms McNaughton said. "We certainly couldn't have the kindy open while the toilets were inoperable".
The school had to close halfway through the day on Wednesday, and remained closed on Thursday as the water level was still too high to use the toilets.
Ms McNaughton said parents had been very understanding of the situation.
"There was a really good system in place for communicating with parents, and letting them know what had happened," she said.
"We don't make the decision to close the kindy lightly...we know it has a big impact on the families."
Ministry of Education statistics showed in total 47 schools and 21 early learning services across the North Island were closed on Thursday, estimated to have affected 5875 school students and 709 pre-schoolers.
Ministry of Education's deputy secretary of Sector Enablement and Support Katrina Casey said the majority of these had been closed due to flooding on nearby roads.
"There has been no reports of major damage although several schools and ECEs have reported minor damage."