"I have done this every two years for the last eight years. I am amiable with [the students] and there is no animosity. I emphasise that they have done nothing wrong," Mr Kirk said.
A mother of one of the boys kept in the hall this week spoke to the Advocate on the condition of anonymity for her and their son. She was so appalled by what happened to her son that she was considering changing schools.
She said she was not in a financial position to pay the $60 owing to the school until Tuesday next week, as she has had to buy new school shoes, school bags and stationery for her three sons.
"I feel humiliated for him [her son], this is not his problem, it's mine," she said.
Mr Kirk said parents are sent an invoice at the end of each month and asked to pay what they owe.
In December last year a letter was sent to all parents urging them to pay all outstanding fees. If they had not been paid and the school was owed more than $20 the students were taken from class and put in the school hall where they would fill in worksheets under his supervision. Mr Kirk said families that were already on a payment plan and had a good history with paying were excused from the exercise.
The fees were for things that the students had done in previous years - such as sports teams, school trips, Rubicon programmes - and not for the voluntary donation.
Mr Kirk said 95 per cent of parents pay their fees on time, and the hard-line he takes means the school gets back thousands of dollars that have been overdue for years.
"I appreciate it is unpopular, but in my 15 years as headmaster of this school no one has given me another solution," he said.
Katrina Casey, head of sector enablement and support at the Ministry of Education, said the ministry was not aware of this happening at any other school.
"We certainly would never support such action. It would be highly inappropriate and unacceptable for any principal to take the action claimed," she said.
Senior solicitor for YouthLaw Jennifer Puah said all children were entitled to a free education under the Education Act 1989.
"Excluding such children from usual mainstream curriculum education may constitute discrimination against a student due to their family status," Ms Puah said in a statement to the Advocate.
Ms Puah said YouthLaw receives queries about this kind of exclusion on their information line reasonably often. She encouraged any students who had questions to call 0800UTHLAW.