The range of symptoms included nausea, vomiting, stomach pain and a slightly raised temperature.
At least five ambulances and eight fire engines went to the school.
Wellington Free Ambulance said 40 children who had "very minor" symptoms were treated at the school by paramedics.
Ten others with moderate symptoms were taken to Wairarapa Hospital in Masterton.
Fire and Emergency said about 100 children at the school were triaged and put through a decontamination process. Parents were asked to bring a change of clothes for their children.
By 7pm, the last of the 10 who were taken to hospital had been discharged, a hospital spokeswoman said.
She expected the regional public health service would be involved in trying to locate the source of the problem.
Police said inquiries were ongoing to find the source. They were door knocking in the area and investigating the school grounds.
A Fire and Emergency spokesman, commenting on reports of a substance coming from a plane, said, "... that's been unsubstantiated at this stage and we don't believe it's come from a plane … we just don't know where it's come from. That's a mystery to us at the moment."