The graphic footage that circulated on Indonesian social media in recent days, showed several people assaulting a man in the eastern region, with his hands tied in a water-filled steel drum.
The eastern region is where separatists have waged a decades-long insurgency against Indonesian forces.
Another video showed the same man shivering in the drum while a man in fatigues slashes his back with a combat knife.
The military opened a probe into the incident after the footage spread and detained 13 soldiers out of more than 40 questioned, military spokesman Kristomei Sianturi told a press conference.
"Out of those 42 soldiers, indications were found that 13 soldiers committed the violent act," Kristomei said.
The soldiers will soon be named as suspects, he added.
The attack allegedly occurred last month but the video went viral last week.
Izak Pangemanan, a senior Indonesian military official in Papua, said the actions of the alleged perpetrators "tarnished efforts to handle conflict in Papua" and apologised for the incident.
"I apologise to all Papuan people. And we will continue to work so that these kinds of events will not be repeated in the future," he said.
Military officials said the man was accused of planning to burn down a health clinic and was a member of an armed criminal group, an Indonesian army term for describing Papuan rebel groups.
Papua's main rebel group has claimed responsibility for attacks against soldiers and civilians in recent years.
Indonesian security forces have for years been dogged by allegations of rights abuses against Papua's ethnic Melanesian population including extrajudicial killings of activists and peaceful protestors in their efforts to crush the rebel groups.
Papua is the Indonesian region that shares a border with independent Papua New Guinea on the island of New Guinea, just north of Australia.
The former Dutch colony declared independence in 1961, but neighbouring Indonesia took control two years later, promising a referendum.
In 1969, a thousand Papuans voted to integrate into Indonesia in a United Nations-backed vote.
Papuan independence activists regularly criticise the vote and call for fresh polls, but Jakarta says its sovereignty over Papua is supported by the UN.
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