The boy, 10, was found trapped under the structure in St Lucy's School in Wahroonga about 2pm on Wednesday.
A rescue operation was attempted by Fire and Rescue NSW but the boy died at the scene, police said.
The school, which will remain closed until further notice, said it was very sad to confirm "the tragic death of one of our students".
"We are cooperating with investigating police and are not able to make any further statement today," a spokesman said.
"We ask for privacy and space for our staff and families to grieve at this difficult time as we remember our beautiful student."
Attempts to recover his body began in the late afternoon and were expected to take several hours.
Police have established a crime scene at the school, which provides primary and high school education for children with disabilities.
Established in 1938 as a school for blind children, it specialises in a range of disabilities including intellectual disabilities, autism and sensory impairments.
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