Thai officials said the event, which was halted minutes before it was due to start, could have affected relations between the two countries.
The HRW report focuses on the treatment of a Christian group in Vietnam.
The group said the Thai response showed how freedom of speech had been eroded since the army seized power last year.
Thai police said the event at the Foreign Correspondents Club of Thailand could "have an impact on the country's security or could affect the friendship and cooperation between Thailand and Vietnam".
It is the third human rights event at the venue that has been halted by authorities in the past month.
The HRW report describes what it says is the persecution of Montagnard Christians in Vietnam's central highlands. Their religious practices have been described by the Vietnamese government as "evil".
Sunai Phasuk, Human Rights Watch's senior researcher in Asia, said the decision to cancel the report's launch was "very disappointing".
"Thailand is now going to be known as the defender of human rights violators in [Southeast Asia], which adds more damage to Thailand's already tarnished international reputation under the military rule," he added.
Thai authorities have launched a crackdown on critics since the military seized power from a civilian government in May 2014.
Thailand's military-run government has forced Human Rights Watch (HRW) to cancel an event in Bangkok to launch a report into alleged abuses in Vietnam.