The lockdown at Tamahere Model Country School, on the outskirts of Hamilton, has been lifted.
Police were called to the school after senior students saw a stranger behind the school grounds wearing a balaclava and carrying what appeared to be a shotgun, an update from the school to parents said.
The lockdown was lifted after police inspected the school grounds and the area where the stranger was spotted and did not find anything.
Parents who turned up at the school reported seeing the Armed Offenders Squad and police dogs at the school.
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In an earlier email to parents just after 1.30pm, the school advised that children had all been accounted for and were safely locked inside.
A police media spokesman said at least two police units arrived at the school and spoke with the principal and students who told police the balaclava wearing man was acting suspiciously on school grounds.
Police will put on extra patrols at the school over the next few days.
Police were called to the school at 1.20pm.
An earlier note from the school said it hoped it was a false alarm, but was "erring on the side of caution".
"We are pleased with how our staff and students have responded to this process and will always take the cautious approach with regard to such reports."
The school finishes at 2.30pm, but parents were advised the event could disrupt school pick up.