Phelps, now a pastor at another IFB church, told "20/20" that Anderson voluntarily stood before the congregation in 1997, that he reported Willis to the Concord Police and complied with all legal requirements of him at the time.
After she announced she was pregnant, Phelps and Anderson's mother arranged to send her thousands of miles away to Colorado to live with another IFB family.
In his testimony this week, Phelps said he did not notify police that Anderson was leaving the state for Colorado but added, "I didn't whisk her away...I've been thrown under the bus on this thing."
Leaf, Anderson's mother, testified that she did not support her daughter's allegations, saying "I only support the truth, not a lie."
In March 1998, Anderson gave birth to a baby girl. Adoption records show that Willis admitted he was the father.
Thirteen years after the alleged crime, Matt Barnhart, a former member of Anderson's church, who was present when she confessed to being pregnant in 1997, wrote a post referencing her story on a Facebook page called, "Independent Fundamental Baptist (IFB) Cult Survivors (And their Supporters)."
Barnhart told "20/20" that Anderson's confession bothered him for years but he felt he couldn't speak out about it.
"The whole culture is you don't question the ministry, you don't question the pastor," he said.
The IFB Facebook page supervisor, who runs an advocacy group for former IFB members, alerted Concord, N.H., police.
Anderson, who at the time was teaching voice at the International Baptist College in Chandler, Ariz., said she got the call from police out of the blue. Since making her allegations public, Anderson has lost her job, The Concord Monitor reported.
In her April interview with 20/20, Anderson said that, despite her traumatic experiences, she hasn't abandoned her faith. Anderson, who is married now and has three more children, says she knows what to tell them about that dark chapter in her life.
"I would just say, 'Mommy went through a time where some bad people did some, some tough things ...but we've made it through,'" she said, "'and God is still good.'"