One of the lawyers for the civil suit, Stewart Ryan, said: "It is alleged [in the suit] that our clients reported the sexual assaults to Scientology at the times that they happened. It is alleged in the suit that Scientology attempted to cover up the sexual assaults."
The church has denied all the civil suit claims against it to the New York Post.
One alleged survivor, identified by name in the criminal filing as Chrissie Carnell Bixler, dated Masterson from 1996 until 2001 and claimed to have been drugged and raped, multiple times, in the actor's Hollywood Hills home.
According to the amended civil complaint: "On more than one occasion Plaintiff Bixler awoke in bed to find Masterson sexually assaulting her. In one specific instance, Masterson drugged … Bixler's wine at dinner and ... assaulted her. The following morning, Masterson admitted that he had anal sex with her while she was unconscious."
Masterson has maintained his innocence of all civil and criminal charges. If convicted, the actor could be sentenced to a maximum term of life imprisonment.
His lawyer Thomas Mesereau said the actor was "in complete shock" over the "nearly 20-year-old allegations."
However, former Scientologist believed that the accusations were delayed as it would have been challenging for authorities to gain co-operation from alleged victims while they remained affiliated with the church.
Ex-Scientologist Geoff Levin alleged that in situations like this, the church would have dealt with the allegations in house as part of its protocol and the woman would have undergone "security checks".
"Maybe you'd be directed into finding that, 10 million years ago, you enslaved a whole city and allowed your soldiers to rape all the women," Levin added. "[And] that is the reason why this is happening to you now. It is brainwashing to the Nth degree."
Ryan, the lawyer, told The New York Post that it "is accurate" that the women experienced intimidation tactics by the church.
"It was part of the pressure campaign to force them into silence."
The civil suit details allegation of such tactic, including Bixler claiming she was stalked by church members.
She also claimed she caught on film "an agent of [Scientology]" spitting on her after he caught him trying to hack her phone and that there were threats to leak nude photos of an underage Bixler.
According to the suit, she also believed that Scientology representatives contributed to the deaths of two of her family's pets.
Scientology has always been a family affair for Masterson. His parents too were members of the church.
It didn't take long for him to establish himself as a famous face of the church and headline several fundraising events.
His celebrity status also meant his family was welcome at the church's Celebrity Centre.
"Danny was part of the young Hollywood clique. He ran with Jason Lee [who has since left the church], Giovanni Ribisi, Laura Prepon and [Grounded for Life] sitcom actress Lynsey Bartilson," Levin said.
"I think the Hollywood environment changed [Danny]. Lots of freedom and partying … Scientology unfortunately treats its celebrities and big-money donors differently. They will let various celebrities get away with s**t and turn a blind eye," a family source told the New York Post.
A representative for the church denied these claims.
The question is whether the church will stand by the actor if he is convicted.
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