The site was hacked on Thursday and Friday by a group calling itself the Sri Lanka Youth.
It demanded that A-level exams due to be held in April be rescheduled because they clashed with Sinhala and Tamil New Year celebrations.
The student, 17, is being questioned to determine any other motives.
A message posted by the group in Sinhala protested about new exam times and called on the president "to take care of the security of Sri Lankan websites or... face a cyber war".
