The boy attended the Spirit of Hope Kinder-prep in St Andrew.
Sara Martin, general secretary of the YMCA, told The Gleaner the organisation was deeply saddened by the incident and would be working closely with the school to provide counselling for students and teachers.
Lesson had finished
Martin said six students had just finished a lesson when the pool was cleared, the whistle was blown and the students were sent to shower.
"They were checked off and handed back over to their teacher who then noticed that the student was missing," she said.
Checks were made and the child was found at the bottom of the pool.