Before his 2009 death, Jackson denied repeated, similar allegations against him, and his estate has denounced the documentary.
Leaving Neverland was also nominated for three additional awards in picture editing, sound editing and sound mixing.
Director Dan Reed, who was also nominated for Outstanding Direction of a Documentary/Nonfiction Program, thanked Safechuck and Robson during his acceptance speech.
“This has been quite a journey for this doc. It began with an obscure reference in a web page to two young men I’d never heard of before,” Reed said, according to Deadline.
WATCH: Jermaine Jackson speaks out against ‘Leaving Neverland’ documentary
“None of this would have been possible without the incredible courage and determination of Wade and James and their families, and I wanted to salute that,” Reed said.
“This is one of the first times we’ve been able to shine light on child sexual abuse … The pattern of how it unfolds is not an easy story to tell … It often remains undisclosed for so many decades so I thank them from the bottom of my heart,” the director said, also thanking Channel 4 and HBO for their “unwavering support for this very difficult production.”
Jackson’s estate criticized the HBO documentary’s win in a statement to Entertainment Tonight.
“For a film that is a complete fiction to be honoured in a nonfiction Emmy category is a complete farce,” the statement read.
“Not one shred of proof supports this completely one-sided, so-called documentary, which was made in secrecy and for which not one person outside of the two subjects and their families were interviewed,” the Jackson estate claimed in the statement.
Jackson’s estate previously filed a lawsuit against HBO, asking for US$100 million.
WATCH: ‘Leaving Neverland’ — Michael Jackson’s legacy facing new sex abuse claims in HBO doc
The lawsuit, filed in Los Angeles Superior Court, alleged that by co-producing and airing Leaving Neverland, the cable channel was breaching a deal to not disparage the singer.
The allegedly “breached” deal in question dates back to 1992. It allowed HBO to air Michael Jackson in Concert in Bucharest: The Dangerous Tour and included language that the channel would not disparage the singer at any future point.
According to Variety, however, the TV network is “immune from a defamation claim,” as Jackson died a decade ago. HBO is now reportedly hitting back against the estate, rebutting claims of a contract breach.
According to HBO attorneys Daniel Petrocelli and Theodore Boutrous, HBO’s contract with Jackson expired once the company fulfilled its obligations of airing the 1992 concert film.
Jackson was never once disparaged in the time HBO aired the concert film, they argue. The last time it aired through their network was in October 1992, which the lawyers suggested would have marked the official end of their deal.
As of this writing, the legal dispute between the Jackson estate and HBO is ongoing.
WATCH: A timeline of Michael Jackson’s sexual abuse allegations
To this day, the truth about Jackson remains unknown, but the singer was never found guilty of any crime in a court of law.
Jackson denied all sexual assault accusations throughout his life, and since his death, he’s been unable to defend himself in the court of public opinion.
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