One Twitter user wrote that "her outpourings of supposed empathy and solidarity to the [metoo] movement don't quite ring true since she is still a prominent Scientologist - an organisation which silences women more than any other."
Another said: "Elisabeth Moss winning for Handmaid's Tale, and then giving a speech about injustice and inequality, all while being a proud Scientologist is GOLDEN."
According to Fox News, the church has come under fire recently amid claims it had knowledge of rape claims made against Scientologist actor Danny Masterson long before reports became public in the media.
In November, it was reported that four women had come forward to accuse Masterson of sex attacks.
The historic claims against the 41-year-old all dated back to the early 2000s.
The women, all members of the Church of Scientology, also claim that the organization covered up the alleged sexual assaults by Masterson, a fellow Scientologist. Masterson has denied all the accusations against him.
The case began in 2004 when a woman filed a report with the Los Angeles Police Department saying Masterson raped her when she was 'passed out' in an earlier incident in 2003.
She claims she woke up when she realized what was happening but he choked her until she passed out again. However, the case was eventually closed after the Church of Scientology submitted over 50 affidavits from Scientologists who denied the woman's account.
In a December statement released to the media the church said it "adamantly denies" ever ignoring any allegations of criminal behavior "especially at the expense of alleged victims".
"What is being stated is utterly untrue. This has nothing to do with religion. This story is being manipulated to push a bigoted agenda. The church follows all laws and cooperates with law enforcement. Any statement or implication to the contrary is false.
The police report detailing the alleged assault from one victim were obtained by The Underground Bunker.
The woman claimed that the church had "threatened her" and if she told the police she would "lose everything and everyone".
She added in her statement to police: "Then they put me on a massive ethics program as punishment. My rapist was not punished at all.
"They didn't even call him to talk about it. I ended up breaking up with him two months later."
In Scientology, reporting another church member to law enforcement is considered a "suppressive act" and which can lead to punishment or even expulsion from the church.
Sources familiar with the case told Buzzfeed, the woman's file had mysteriously vanished in 2004, leaving Deputy District Attorney Reinhold Mueller to reconstruct it.
The other three women allegedly reported their rapes directly to the Church of Scientology.
Moss was raised as a Scientologist and in 2013 said that it gave her stability and empowerment and helped her learn to respect herself.
When asked about her support in 2014, however, Moss would not answer questions about the religion.
Last year, the former Mad Men star responded to a comment about Scientology on Instagram having written about her role in the Last Handmaids Tale.
And while the post initially garnered positive responses, Instagram user @moeleybanks decided to ask a question which compared Gilead, the authoritarian state depicted in The Handmaid's Tale, to Scientology.
"Love this adaptation so much. Question though, does it make you think twice about Scientology?" asked @moeleybanks. "Gilead and Scientology both believe that all outside sources (aka news) are wrong and evil… it's just very interesting."
While Moss usually avoids talking about her religion, on this occasion she responded to the question.
"@Moeleybanks That's actually not true at all about Scientology," she wrote.
"Religious freedom and tolerance and understanding the truth and equals rights for every race, religion and creed are extremely important to me. The most important things to me probably. And so Gilead and THT hit me on a very personal level. Thanks for the interesting question!"
In her speech on Sunday, Moss paid tribute to Margaret Atwood by reading a message from the author about female empowerment.
"We were the people who were not in the papers," read Moss. "We lived in the blank white spaces at the edge of print. It gave us more freedom. We lived in the gaps between the story."
Moss then dedicated the award to Atwood.
"Margaret Atwood, this is for you and the women who came before you and after you who were brave enough to speak out against intolerance and injustice" the Mad men actress continued.
"We no longer live in the blank white spaces at the edge of print. We no longer live in the gaps between the stories.
"We are the story in print. We are writing the story ourselves." she concluded.
