The private Waikato school, which is being investigated for workplace bullying, was closed after the threat, which saw students evacuated from the campus.
Those residing in the school's boarding houses on the rural campus sheltered at a nearby sporting complex on Thursday night.
Parents were told by email at 10.30pm alerting them about the threat.
St Peter's School in Cambridge is the largest co-educational boarding school in New Zealand.
The school has been in the news this week after the abrupt departure of executive principal Dale Burden and his wife, and deputy principal, Yevette Williams.
It emerged last week that anonymous bullying complaints were made to workplace watchdog WorkSafe last term.
At least two inquiries are now under way into the allegations with the school board hiring two independent investigators.
Board chairman John Erkkila said the investigations would try to find out what may or may not have occurred and has reassured parents the matter was being taken very seriously.
"And I want to understand, if any wrongdoing is found, how that was allowed to happen and how we go about ensuring it doesn't happen again.
"But if it is deemed that workplace bullying has occurred, I want you to know that it will be addressed.
"I cannot and will not allow bullying of any kind in our workplace. Being on the receiving end of bullying behaviour is incredibly damaging to a person's mental health and it will not be tolerated, now or ever."
WorkSafe confirmed it was making inquiries about "staff wellbeing" at the school amid the absence of Burden and Williams.
The pair left the school sometime towards the end of term one.
