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.
Video of the incident that circulated online over the weekend shows a man with a snake draped around his neck as officers taunt him, ordering him to admit to the theft or face having the reptile put in his mouth or his trousers.
Throughout the interrogation, officers can be heard asking: "How many times have you stolen mobile phones!?"
The suspect later responds: "Only two times".
The video shows a Papuan man in custody, screaming in terror at a large live snake wrapped around his neck and waist while his interrogator laughs.
A voice in the video reportedly threatens to put the snake in the man's mouth and down his pants. "The investigator was not professional in doing his job", Swadaya admitted.
Papua province's police spokesman said the officers involved are being questioned by an internal affairs division of the national police.
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"We apologise for the incident", he told AP.
"The snake was tame and not poisonous or unsafe, and the incident was their own idea so they could get admission of guilt as quick as possible", Swadaya said in a statement.
Tonny Ananda Swadaya, the police chief in Jayawijaya district, where the incident took place, apologised in a statement yesterday.
Reports of human rights abuses are common from Papua, where separatists have long sought independence from Indonesia.
Human rights lawyer Veronica Koman, who circulated the video, said that the interrogation methods were torture and violated police policies as well as several laws.
Koman has said a snake was also used during the interrogation of one of her clients in January. The former Dutch colony was made a part of Indonesia after a widely criticized UN-backed referendum in 1969. Such efforts have intensified after rebel militants killed 19 people working on the construction of a trans-Papua highway project in December 2018.