Basyle “Boz” Tchividjian has devoted most of his career to an emotionally and spiritually wrenching task.

A former prosecutor, he’s been investigating charges of sexual misconduct and child abuse for nearly three decades. Since the mid-2000s, however, he’s focused on American houses of worship, especially those within his own evangelical Protestant tradition. He’s handled hundreds of cases over the years, and he is still seared by the memories of them.

There was the missionary boarding school in Africa his team investigated, in which house parents and teachers were abusing a number of children. “It was an eye opener for us, we left our soul behind after the investigation,” says Mr. Tchividjian, who in 2003 founded an organization called GRACE, or Godly Response to Abuse in the Christian Environment.

While the #MeToo movement has revealed widespread abuse from Hollywood to government to businesses, mounting allegations of sexual misconduct within houses of worship and religious communities point to something perhaps even more appalling – a breach of a special trust. And a number of activists suggest it is far more common than many may imagine.

“In the early 2000s, when the tragedy of the Catholic Church was just starting to emerge, I’m thinking to myself, and sharing with others, my goodness, Protestants for the most part have no clue that this is as serious as an issue in their own churches,” says Tchividjian, a grandson of the historic evangelist Billy Graham and a law professor at Liberty University in Lynchburg, Va.

During the past year, many women, and even some men, across the country have used the online hashtag #ChurchToo to tell their stories of past abuse. They have recounted how men in power used their uniquely intimate roles as pastors to spiritually manipulate and sexually coerce them when they were at their most vulnerable. Many were underage teens.

“Women who have paid this pound of flesh for years, and have not been heard, or who have been silenced, are finding this kairos moment,” says Belinda Bauman, founder of One Million Thumbprints, a global campaign to assist women affected by war. Kairos is a theological term referring to a crucial moment to take action, and Ms. Bauman adds: “Honestly, it feels like we have an opportunity to make a choice right now, and heaven help us if we choose wrongly, for the sake of the church and culture.”

High-profile cases

Last week, one of the nation’s most influential evangelical pastors, Bill Hybels, a best-selling author and pioneer of the suburban “megachurch” movement, resigned his position from Willow Creek Community Church in Illinois. Among the allegations against him were suggestive comments, extended hugs, an unwanted kiss, and invitations to hotel rooms from at least two women who were church leaders at the time. Pastor Hybels called such accusations, which had previously led to an internal church investigation, “flat-out lies.”

A well-known Alabama evangelist and author, Acton Bowen, was arrested last week after being charged with child sex abuse. Last month, the president of the Southern Baptist Convention Executive Committee, Frank Page, resigned after admitting to a “a morally inappropriate relationship.” Earlier this year, too, the Memphis megachurch pastor Andy Savage admitted he had engaged in a “sexual incident” with an underage teen in 1998, after the woman shared her #ChurchToo story online. His congregation gave him a standing ovation after his public confession, but last month he resigned.

“No one is surprised at any of this,” says Bauman, who last year helped to organize a corollary of the #ChurchToo movement called #SilenceIsNotSpiritual.

“We hope and wish and pray and, technically, we even believe that the church should have a whole different standard to measure up to,” she says. “Except that, we’re full of human beings, and human beings in a power structure that has traditionally lent itself to what we call ‘systemic unholiness.’ ”

Why ‘I lost my church’

Her definition of “systemic unholiness” is not simply about abusive pastoring. It also touches on the cultural and institutional attraction to stories of forgiveness and redemption, which in these cases serve only to silence those abused. “That looks a lot like the protection of power, and the protection of men in that power structure, at the expense of women telling their stories,” says Bauman.

Last year, attorney and advocate Rachael Denhollander was the first of nearly 160 women to reveal publicly that she had been abused by Larry Nassar, the team doctor for USA Gymnastics, when she was a homeschooled evangelical teen. And while she extended her forgiveness at his sentencing, she also told Christianity Today that if her abuser had been a pastor, she would have been vilified.

“We are very happy to use sexual assault as a convenient whipping block when it’s outside our community,” Ms. Denhollander said. “When the Penn State scandal broke, prominent evangelical leaders were very, very quick to call for accountability, to call for change.”

But she was asked to leave her church, she said, for being so outspoken on the issue. “The reason I lost my church was not specifically because I spoke up,” she explained. “It was because we were advocating for other victims of sexual assault within the evangelical community, crimes which had been perpetrated by people in the church and whose abuse had been enabled, very clearly, by prominent leaders in the evangelical community.”

Protecting the powerful

When Tchividjian was a prosecutor in central Florida in the 1990s, he was already insisting that his district establish a new special unit to prosecute cases of sexual violence. By the time he left, his office had handled thousands of abuse cases, and Tchividjian says many involved a faith community – one of the reasons he decided to launch GRACE, he says.

“It was just amazing how many church leaders and church members had no problem coming to court and testifying on behalf of the character of the defendant, and how few came in defense of the victim,” he says.

He estimates that he and fellow prosecutors observed this in about 9 out of 10 cases. “There’s something wrong with that,” he adds. “The Jesus that I know was always on the side of the wounded and the marginalized, and that’s not what’s happening here.”

“We are still drawn and seduced by power and influence,” says Tchividjian. “And so, as a result, when there is abuse within churches and faith communities, children are the ones who often fall through the cracks. The powerful and the influential, the perpetrators, those are the ones that we embrace.”

Where abuse flourishes

When it comes to sexual abuse generally, there are few differences among various faith traditions, says Janet Heimlich, author of “Breaking Their Will, Shedding Light on Religious Child Maltreatment.” But theology and belief systems can play a role in what she calls a "perfect storm" of factors in which abuse can flourish. [Editors note: The characterization of Ms. Heimlich's research has been edited for clarity.]

“What it boils down to is when a religious environment is more authoritarian,” says Heimlich, who also founded the Child-Friendly Faith Project, an national advocacy organization that provides help for survivors and helps educate religious communities. “In some religious communities and environments where there is a strict social hierarchy, where certain people have a whole lot of power and others have next to none – that’s when you start to see problems.”

“That includes whenever there’s a fear-based aspect to the way the community rules are set, or in the way beliefs are structured,” she says. “And when there’s a strict social separatism, when a community keep themselves apart from outer communities – whenever you have these three factors, you’re more likely to see these problems.”

Within such communities, “there is often a distrust of law enforcement, and, I think, a feeling that if law enforcement takes a look under the hood, the entire community will be attacked, and it will reflect poorly on the wider community,” says Kacey McBroom, a partner in the Los Angeles-based law firm Kaedian, LLP, who has worked with separatist-leaning religious communities.

“The feeling was: This is something that should be between the accused and God,” Ms. McBroom continues. “He will have to answer to a higher authority, and not the law.”

Breaking a taboo

Tchividjian and Bauman say religious institutions need to both set clear protocols and begin to talk about the issue, which has long been taboo.

“When I speak with pastors, when I speak with Christian leaders, college presidents, a lot of them think this really isn’t their issue,” says Bauman, who, like Tchividjian, has distanced herself from her evangelical heritage. “And I would say, ‘It absolutely is your issue, because 1 in 5 women on college campuses have experienced a violent incident, sexually-based, in their lives,’ ” she says, citing statistics from the United States Justice Department. “And that’s Christian campuses, too.”

“But I love the church, period,” says Bauman. “It is my home. I work in war zones, and I see the damage that the church does globally. But I also see the joy and the healing that the church does globally.”

Which is one of the reasons Tchividjian and his colleagues at GRACE have been trying to develop seminary curricula and training for communities of faith.

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“If we’re going to change the culture of churches, we can’t just go in and do a weekend training on child protection or sexual violence,” says Tchividjian. “What happens with those, you go in for a weekend, you do a training, everyone feels sort of good that they’ve done this, they know a little more, which is good.”

“But at the end of the day, if I go back to the church six months later, and I ask, how has this training impacted the culture of this church carries on business?” he says. “Most of the time, if we’re being honest, not much.”