Morrinsville College principal John Inger was pleased those responsible had been caught and were being dealt with by police.
"That's great that they have solved it, I just hope that it wasn't one of our own [students]."
Mr Inger said the person who fired the shot was "clearly someone irresponsible who didn't think about the potential danger for others and I'm just glad that nobody was hurt".
Earlier, Mr Inger labelled the suspected shooter a "clown".
The school buses will operate as per normal today, he said.
"Oh yes, this is a one-off , we're not in a cowboy town."
The Ministry of Education's head of education infrastructure service Jerome Sheppard confirmed it was investigating the incident.
"We would be very concerned if someone had deliberately shot at a school bus. That would be dangerous and irresponsible. It's really important to us that students can travel safely between school and home, and it's lucky no one was hurt.
"We are investigating the incident, and the bus company has advised us that the driver initially stopped the bus when one of the windows was damaged. The driver confirmed that all students on the bus were fine, and then completed the route."