The eponymous host of Believer with Reza Aslan was in India to meet with ascetic members of the Aghori sect, which has fewer than 100 members.
He also drank from a human skull and was pelted with faeces by a guru.
The footage prompted a backlash from critics who accused him of painting a false and extreme picture of Hinduism, with America's only Hindu Member of Congress tweeting: "I am very disturbed that CNN is using its power and influence to increase people’s misunderstanding and fear of Hinduism."
The Iranian-born religious studies scholar was in India's spiritual capital, Varanasi, which is located on the banks of the sacred Ganges river.
Filming with the Aghori gurus, he also smeared the ash of a cremated body on his face and drank from a human skull.
After Mr Aslan fell out with one of the hermits, the devotee of Shiva began eating his own faeces and hurling it at the presenter, yelling: "I will cut your head off if you keep talking so much".
The Aghori were described as "cannibals" by CNN when promoting the documentary, though they only eat the flesh of people who have died of natural causes.
They believe they can remove the bonds of shame and fear by recognising that all oppositions are ultimately illusory, and their rituals aim to break taboos around body fluids, sexual practices and the dead.
Many live in burial grounds, and they may consume marijuana to aid them in their meditation.
Their extreme devotion to the deity Shiva is said to earn them the respect of rural Hindu populations around Varanasi in the state of Uttar Pradesh.
However, such practices have no place in mainstream Hinduism as practised by around a billion members of the world's third-largest religion, including Member of Congress for Hawaii Tulsi Gabbard.
As well as the first Hindu, Ms Gabbard is the first American Samoan elected to Congress, and was at one time the youngest woman in the legislative body.
Continuing her condemnation of the programme on Twitter, she wrote: "Aslan apparently sought to find sensationalist and absurd ways to portray Hinduism.
"Aslan and CNN didn't just throw a harsh light on a sect of wandering ascetics to create shocking visuals—as if touring a zoo—but repeated false stereotypes about caste, karma and reincarnation that Hindus have been combating tirelessly.
"CNN promotional materials and trailers that included a scene showing a group of Hindus under a caption “CANNIBALS,” perpetuated bizarre and ugly impressions of Hindus and their religion."
She also noted that Hindus are "still reeling after witnessing terrible hate crimes in the last few weeks."
Most recently, Indian-born Harnish Patel was shot dead in South Carolina.
His death follows that of Srinivas Kuchibhotla, allegedly murdered last month by a white man who shouted "get out of my country".
These incidents were also cited in a statement from the Hindu American foundation.
They wrote: "When the knowledge deficit is so stark, and minority communities are facing a rise in hate incidents across the US... why would Aslan and CNN sensationalize the Aghoris as a primetime introduction to the faith of a billion Hindus, most of whom have never seen or met an Aghor?"
But Mr Aslan rejected the suggestion his programme could contribute to a climate of anti-Hindu sentiment, writing on Facebook: "as I repeatedly state on camera and in voice-over, [the Aghori] are not representative of Hinduism but are instead an extreme Hindu sect who reject the fundamental Hindu distinction between purity and pollution.
"In almost every interview I did about the show I talked at length about the issue underlying the episode, including the fluidity of the caste system, the problems inherent amongst the untouchable class, and how devout Hindus of all stripes are working tirelessly to overcome both."
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