Tokomairiro High School, in the South Otago town of Milton, is now out of lockdown.
Police earlier asked the school to keep children inside because a man in the area was brandishing weapons and knives.
The school's office manager Connie Smith said "police asked the school to go into lockdown about 1.15pm.
But principal Glenis Sim said they have now been told to lift the lockdown.
A police spokeswoman said the armed offenders squad had been on the way to Milton but has now been stood down.
A person is in custody and being spoken to by police, she said.