The teacher at a nursery and primary school in Asaba, Delta State, was alleged to have left several marks on the toddler’s body after flogging him last Monday.
The suspect, who is thought to be the son of the owner of the private school, allegedly started beating the pupil after he caught him playing with water.
He has not been reported to have commented on the incident.
The pupil was said to have fallen ill after the incident and was taken to the Federal Medical Centre (FMC) in Asaba where he eventually died.
Police spokesman DSP Dafe Bright told BBC Pidgin that the suspect would be charged for murder and manslaughter.
Source: BBC