The teacher sought advice from the principal who told him to find the student.
The student turned up in his music lesson soon after. Mr Karklins tried to ignore the student but he then lost his temper, forcibly removing him from the classroom.
"He did so by walking up to the student, picking him up, and taking him to the cloak room, where he deposited him on the floor," the tribunal said.
"At this time the student was thrashing around. In the process of being set down on the cloakroom floor, the student banged his head against the wall."
Mr Karklins admitted he acted inappropriately and had lifted the student up "in anger".
Principal Martin Van Rijswijk said both the school and Mr Karklins accepted the tribunal's findings.
He said Mr Karklins deeply regretted what happened and had fully cooperated with the school's investigation into the incident, as well as the subsequent tribunal investigation.
"Over the past year, the school has worked closely with Mr Karklins to ensure that there is not a repeat of this type of behaviour. The school has also unreservedly apologised to the family of the boy," Mr Van Rijswijk said.
The censure will remain on the teacher's register until his practising certificate expires in April next year.
The council also ordered Mr Karklins to pay half the costs of the tribunal and half the costs of the Complaints Assessment Committee.