Fifteen-year-old Grant Stranaghan from Rathcoole was suspended for two days last week for failing to comply with the school's regulations about hair length.
The school has been publicly criticised for its stance by Grant's father, George Stranaghan. However, headmaster David Knox said that the decision to suspend the GCSE student had been taken "only after all other sanctions had failed to prompt a positive response".
Mr Stranaghan claims that the hair cut controversy is now affecting his son's health.
The 45-year-old said that since his son started getting "unwanted attention" at school about his hair being two inches below his shirt collar, he has had to be taken to see doctors about migraines.
"I put this all down to what has happened over his hair – what does it take for the lad to be given a break?
"I have had long hair in a ponytail for many years and it has not done me any harm," he said.
Mr Stranaghan, who spoke earlier this week on BBC Radio Ulster's Nolan Show, added: "This ongoing debacle should not be allowed to affect my son's health.
"He should not have ongoing migraines from stress at his age. He is a straight-A student and very keen on a career working with computers.
"He wanted to be able to put his hair in a ponytail and then put the ponytail down the back of his shirt but the school was not happy with that.
"At 15 years old, you can't hold the lad down and cut his hair.
"He wants it the way it is and I am not going to make him cut it – I don't see this as a major issue."
Mr Knox confirmed that Grant had been suspended under the school's discipline policy for "repeated and persistent breaches of the rules".
"This action is unusual in this school where there is a high level of co-operation from our pupils. The suspension was for two days only and was imposed only after all other sanctions had failed to prompt a positive response," he said.
Mr Knox revealed that he had hoped to discuss the way forward on the issue with Grant's parents, but that his offer to meet with them earlier this week had been declined.
"The school has at all times attempted to be reasonable in this matter while implementing the policies of the Board of Governors who represent parents, teachers and the community. The school wishes to negotiate a reasonable resolution to this problem with the pupil and his parents - one that will ensure fairness and equity for all the pupils and be to the satisfaction of all the stakeholders," he concluded.