Nelson Intermediate School has been evacuated on the advice of police.
In a post on Facebook, the school said it was a precautionary measure for health and safety.
Everyone was safe and well, it said.
"As a result, school will be closed for the day... could you please come and collect your children from the Broads Fields on Tipahi Street, opposite the hospital as soon as possible."
In a statement, police said they were making enquiries after several schools received "an email of a concerning nature".
The threats were taken seriously and "however at this time we do not believe there is a genuine risk".
Police were at the schools, several of which have been evacuated as a precaution, they said.
"Traffic has been impacted by cordons in some places, and we ask motorists for their patience at this time."
A second school nearby, Victory Primary, has also been evacuated, Stuff reported.
Nelson mayor Nick Smith has posted on Facebook, saying he is concerned about the threats made to the schools.
"This disruption and extra stress is the last thing our students, teachers, principals and parents need in the last week of term before Christmas.
"The police and our schools have Nelson's full support as they manage this threat, keep our children safe and work to identify and hold to account the perpetrator," Smith said.
