Officers in the video laugh as an interrogator drapes the animal on a screaming, handcuffed man in the eastern Papua region.
The suspect was believed to have stolen mobile phones.
The local police chief said it was unprofessional but defended the practice, saying the snake was tame and non-venomous.
"We have taken stern action against the personnel," Tonny Ananda Swadaya reportedly said in a statement, adding that the officers had not physically beaten the man.
They had acted on their own initiative to try to draw a confession from the suspect, he said.