The boy's father later said the child may have climbed out of the window to escape the angry teacher.
The boy suffered serious head injuries and multiple pelvic fractures.
The Hamas-controlled government has promised a thorough investigation into the incident. The rival Fatah group says the teacher was one of the two thousand sent to local schools by Hamas following a teachers' strike.
Palestinian doctors have asked for the child to be sent for treatment to Tel-Aviv.
On August 24 thousands of Gaza teachers, who are still paid by the Abbas government in the West Bank, went on strike, which Hamas saw as an attempt to disrupt public order in Gaza. All those who took part in the strike action were banned from teaching. Despite the strike, Hamas kept schools running, and hired some 2,200 new teachers and administrators, many of whom lack qualifications.
