The three - including the headteacher - were taken into custody after a police officer stumbled across the incident in south-western Ogun State.
Pictures show at least two young people - one boy and one girl - tied to a makeshift crucifix with green string.
A police spokesman described the punishment as "a barbaric act".
Local reports say they were being punished for being late.
The officer - named only as Livinus - tried to intervene, asking the school's owner to free the teenagers. When the owner of the school in Ayetoro, 145km (90 miles) north-west of Lagos, refused, the officer decided to take action - only to be forced back.
"When I tried to untie the pupils, the proprietor and his teachers beat me up," he told Nigerian newspaper Punch. "Before I returned from picking handcuffs from my car, they had grabbed a friend who was with me... and beaten him up with a horsewhip."
The suspects were eventually arrested after back-up arrived on site.....
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