Tina Anderson says the rapes resulted in her becoming pregnant when she was only 15.
She also asserts church officials, led by its now former pastor, covered up the crime.
Ernest Willis was 38 and a church deacon when, authorities now say, he raped Anderson. He's been arrested on sexual assault charges.
Authorities are also probing Anderson's cover-up claim.
Anderson says when she came forward about the alleged rape and eventual pregnancy, church officials, led by now former pastor Chuck Phelps, blamed her. Anderson claims she was forced to stand in front of her congregation and apologize for getting pregnant, and write a letter asking Willis' wife for forgiveness.
She was later sent off to Colorado where, she says, she was forced to give up the baby for adoption.
The case was reopened this year after online posts and friends led police Anderson.
In a gripping interview with co-anchor Chris Wragge on "The Early Show on Saturday Morning," Anderson added that the former church officials are still blaming her - and said she fears they would do the same thing to someone else. She also said they tried to "brainwash" her to make believe it really was her fault.
Willis is out on bail and has another court appearance slated for June 16.
Police have said their 1997 investigation was shelved because they couldn't locate the victim, and they are now investigating how much church leaders knew about the allegations.
Phelps says he reported the rape allegations to police and child welfare officials within a day of hearing about them from Anderson at the time and did nothing to conceal her whereabouts. He said he also told Willis he was calling the police and advised him to turn himself in.
"I never once got a call from the Concord police. ... They simply didn't do anything. This is unconscionable, what's happening to the Church here and to my reputation," Phelps, now a pastor in Indianapolis, said Thursday.
Phelps also contends it was Anderson's mother who decided to move her to Colorado, while his role consisted of helping find a family for her to live with.
Anderson told Wragge she was "in complete shock when I got the call" from police when the probe was re-opened. "I never expected it. And it's been very tough. It's been very emotional and very overwhelming to go through it all again.
"I've sought to move on," an emotional Anderson said. "There's always something there, there's always heartache there, but I've sought to kind of leave that and move on in my life."
Anderson says she thinks, "Justice will be served when (Willis) has his day in court and when he goes to prison. I think that should have happened a long time ago."
But, she added, she thinks, "There are other issues that also need to be addressed in this story, as well.
"Chuck Phelps and Matt Olson did a lot to systemically brainwash me and make me believe this was my fault, to cover things and make people believe that it wasn't Ernie's baby, to make -- even Chuck Phelps' wife, when we came forward, asked me if I enjoyed it when it happened. And it's not OK.
"Matt Olson made me write a letter to Ernie Willis' wife asking for forgiveness for betraying her trust."
All in all, Anderson says, "I'm sad. I'm very sad and I'm heartbroken and I think it's not OK. It's not OK to make victims believe it's their fault. And I think I'm sad because I know they don't think they did anything wrong. They still don't believe that. They still blame me. And I think they'd do to another girl."
If you or someone you know is a victim of abuse, rape or incest, you can get help at the Rape Abuse and Incest National Network.