All religious groups in Vietnam are required by law to register with the Vietnamese government.
Vietnam's indigenous minority Christian community, known collectively as the Montagnards, live in the country's Central Highland provinces and worship in unregistered house churches outside the control of the official Southern Evangelical Church of Vietnam.
The Vietnamese government says the Montagnards, or "Dega Protestants" as it calls them, are not a legitimate religious group but rather a cover for a Montagnard independence movement.
With independent, international rights groups denied access to the region, HRW's report has been compiled using interviews with Montagnards who have fled Vietnam, as well as reports in Vietnam's government-controlled media.
The report warns of a government crackdown on the Montagnards in response to their calls for religious freedom and land rights.
The authorities are accused of rooting out Christians in hiding and dissolving house church gatherings, orchestrating coerced renunciations of faith, and sealing off the border to prevent asylum seekers from fleeing to Cambodia.
"Political security" units are rounding up and interrogating anyone suspected of being a political activist or unregistered house church leader.
HRW says more than 250 Montagnards are in prison or awaiting trial charged with national security crimes, such as "undermining national solidarity".
One man in the report who was sentenced to five years in prison describes how the police used their hands to box both his ears at the same time.
"Blood came out of my ears and my nose. I went crazy from this. It was so painful, and also the build-up made me very afraid and tense," he said.
The unidentified man remains partially deaf as a result of the torture. Other former prisoners and detainees in the report describe being severely beaten.
Phil Robertson, HRW's deputy Asia director, called upon Vietnam to immediately recognise independent religious groups and allow them to practice their beliefs.
"Montagnards face harsh persecution in Vietnam, particularly those who worship in independent house churches, because the authorities don't tolerate religious activity outside their sight or control," he said.
"The Vietnamese government has been steadily tightening the screws on independent Montagnard religious groups, claiming they are using religion to incite unrest."
He added: "Freedom of religion does not mean freedom for state-sanctioned religions only."