The man can be heard hysterically screaming and shouting as the police officers tell him to open his eyes and watch as they threaten to stuff the live reptile into his mouth and down his pants.
The police involved have apologised for using a live snake as part of interrogation methods to deal with petty crime.
A video circulating online showed police in Jayawijaya district wrapping a snake around the neck of the suspect as they questioned him. "Only two times", the prisoner is heard saying, as another man rubs the snake on his face.
Officers appear to be asking how many times he'd stolen cellphones.
They had acted on their own initiative to try to draw a confession from the suspect, he said.
A voice off-camera can be heard ordering the man to keep his eyes open as the snake is pushed towards him.
'We have taken stern action against the personnel, ' he said, adding the officers themselves had not physically attacked the man.More news: Sunday snow leads to more tricky travel Monday, Tuesday
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"We apologise for the incident", Kamal told The Associated Press.
Human rights lawyer Veronica Koman said on Sunday that the interrogation methods were torture and violated police policies as well as several laws and stated that this was only the latest of several reports of police using this method. "Institutionally we do not recognize such an unprofessional method of interrogation, and we guarantee that such an inhuman method will not happen again in the future".
"When this snake video surfaced, many Papuans, particularly activists, who have been in and out of jail for political reasons, said that they have long known that snakes are being used by police and military", she said.
The central government in Jakarta has reportedly committed various human rights violations in its suppression of the independence movement.
The former Dutch colony, the resource-rich western part New Guinea island, was incorporated into Indonesia after a widely criticized UN-backed referendum in 1969.
In December Papuan Governor Lukas Enembe called on the army to leave the state amid a crackdown on rebels fighting for independence.