Get breaking news alerts and special reports. The news and stories that matter, delivered weekday mornings.

The Archbishop of St. Louis is asking Catholics to re-evaluate their relationship with the Girl Scouts based on what he claims is a "troubling pattern of behavior" that is becoming "increasingly incompatible with our Catholic views."

Archbishop Robert J. Carlson of the Archdiocese of St. Louis, addresses a crowd at the Capitol Rotunda in Jefferson City, Mo., on March 27, 2012. Julie Smith / News Tribune via AP

The problem, according to Archbishop Robert Carlson, is the 104-year-old organization's blanket support of transgender and gay rights.

In a letter penned last week, he said that "recent concerns about Girl Scouts USA and their position on and inclusion of transgender and homosexual issues are proving problematic."

Ben Miller, who leads the Youth Outreach for the St. Louis Archdiocese, acknowledged that the Girl Scouts does not promote any specific religious belief — but it was necessary to point out the ideological divide.

"While we’re not saying it’s the Girl Scouts' job to teach the Catholic faith, when there are points that contradict the faith, that’s where we come into a problem," he told NBC News. "Our motivation is concern for our youth."

Among these points of conflict is the Girl Scouts of USA’s recent statement of inclusivity, which welcomes children who are transgender. The Archdiocese wrote that this statement, along with the Girl Scout’s tweet of support for same-sex marriage are proof that “progressive issues are becoming more and more central to the Girl Scout message.”

Let our news meet your inbox. The news and stories that matters, delivered weekday mornings. This site is protected by recaptcha

“We take pride in being inclusive,” Girl Scouts of Eastern Missouri CEO Bonnie Barczykowski told NBC News. “We are accepting of all girls. Girl Scouts have been inclusive since its inception in 1912.”

“It’s disappointing. We’ve had a long history of cooperation with the archdiocese," she added. "We’ve been able to combine the two organizations really well for so many of our girls.”

Connie McNutt’s Girl Scout Troop 1916 is an example of this collaboration. The troop volunteers to help the homeless at St. Patrick Center and has worked with both Girl Scouts and Catholic Charities in the St. Louis area for years.

“In terms of community and service both are very similar. We are more alike than we are different,” McNutt said.

While Miller maintains that “we’re not saying you can’t do Girl Scouts,” Archbishop Carlson announced in his letter the creation of a Catholic Committee for Girls’ Formation to replace the Catholic Committee for Girl Scouts.

Carlson’s letter tells Catholics “we must stop and ask ourselves — ‘is Girl Scouts concerned with the total well-being of our young women?’”

Related: MSNBC: Girl Scouts Deny Discriminatory Donation

To McNutt, the answer is unequivocally yes.

“What Girl Scouts does most is build confidence," she said. "Kids are learning to be generous and kind, not just with things but their time. I wish they’d know that troops are doing great service.”

The Girl Scouts of Eastern Missouri says it has worked with the Archdiocese of St. Louis for nearly 100 years, and there are currently more than 4,000 girls in troops within Catholic schools and parishes.

“We must stop and ask ourselves — ‘is Girl Scouts concerned with the total well-being of our young women?’”

While many Catholic families have already reached out to Girl Scouts voicing their support, McNutt says several families have called expressing their concerns with keeping their children involved in the organization, based on the letter.

Barczykowski has reached out to the St. Louis archbishop directly, hoping that they can sit down to discuss the letter personally. Carlson has not yet responded to her request.

“The bottom line is it’s not about a CEO or an archbishop, it’s about the kids,” McNutt said. “We need to find a common ground. Sometimes you have to take a step back from a situation and see that the kids are the most important.”