The boy had been near D.S. Senanayake Vidyalaya, Colombo after sitting for the first mathematics paper at the GCE ordinary level examination on December 14 when the incident occurred.
He has told the newspaper that a rival group of students had lodged a complaint against him following a clash a few weeks ago.
The complainant is a relative of Maj. Gen. Gunaratne.
The incident was discussed on the following day at a meeting between the principal and members of the old boys association.
One of the old boys said the school would not take any action officially.
CTU to take up the incident
However, Ceylon Teachers Union secretary Joseph Stalin said they would take the student after the examination ends tomorrow to the Sri Lanka Human Rights Commission and to police to lodge a complaint.
The retired major general has told lankacnews website that certain websites were publishing false and baseless reports about him.
He said he had never attacked a student, or never attacked a soldier when he was in the Army, adding that if his information was correct, he was abroad on the day the alleged incident occurred.
He went on to say that the son of his cousin was studying in the school, and a group of students had demanded money from him and assaulted him, about which his parents have lodged a complaint with Cinnamon Gardens police.
An official of Cinnamon Gardens police confirmed receiving a complaint about a clash between two groups of students of the school, but said that no complaint had been received against Gunaratne.