The sometimes tense relationship between the Catholic Church and the Girl Scouts appears to be moving toward a resolution, as the U.S. Conference of Catholic Bishops has asked scout leaders to clarify programs and material that some religious conservatives think promote contraception and abortion.

Potentially at stake is whether troops can continue meeting in Catholic churches, and whether many Catholic girls, who make up a quarter of the nation’s 3 million Girl Scouts, will continue in scouting as the organization marks its 100th year.

In a letter dated March 28, the head of the bishops committee that has been looking into concerns about the Girl Scouts said he wanted to identify and address all remaining questions. The letter was written by Kevin C. Rhoades, bishop of Fort Wayne, who was a leading critic of the University of Notre Dame when it awarded President Obama an honorary degree in 2009.

The Associated Press reported on the letter Thursday, referring to it as an “official inquiry.”

The letter said that “important questions still remain and need to be examined.” But areas of concern were not specified, and church officials declined to be more specific. They characterized the letter as simply asking for further clarification.

“There had been some complaints about the Scouts, and the bishops couldn’t turn a deaf ear,” said Sister Mary Ann Walsh, a spokeswoman for the bishops. “So they want to know, what’s the story?”

The Girl Scouts organization said it expects the questions to be answered to the bishops’ satisfaction.

“We’ve had a strong relationship with the Catholic Church for 98 years,” said Girl Scouts spokeswoman Michelle Tompkins. “We don’t expect it to change.”

Controversies have bubbled up in recent years, many of them rooted in misinformation. The Girl Scouts of the USA has denied any partnership with Planned Parenthood, and says it has no positions on abortion, birth control and sexuality.

But questions, largely spread through Internet blogs, have persisted. Earlier this year, St. Timothy Roman Catholic parish in Chantilly in Fairfax County ousted 12 troops with 115 girls. Lawmakers in Indiana and Alaska publicly berated the Girl Scouts.

Critics of the Girl Scouts contend their materials shouldn’t have any links to groups like the Sierra Club, Doctors Without Borders and Oxfam, or other groups that support family planning and contraception. Other critics are unhappy that the American Girl Scouting organization is a member of an international scouting association that supports contraception access.

Some parents have reported that when their daughters go out to sell Girl Scout cookies, they have had doors slammed in their faces by people refusing to buy their treats because they think the profits go to support abortion and birth control.

For the past two years, the U.S. Conference of Catholic Bishops has had its Committee on Laity, Marriage, Family Life and Youth ask the Girl Scouts to explain their stances and materials.

The Girl Scouts have made modifications, said Robert McCarty, executive director of the National Federation for Catholic Youth Ministry, which has a Web page devoted to debunking rumors about the Girl Scouts.

“The Girl Scouts have been very open to hearing the questions and the critiques,” he said. “They’ve changed some print materials. The materials themselves are usually fine. But if you follow the links, they have the potential to be problematic.”

McCarty said the answers should allow the Girl Scouts and the bishops to put the matter to rest.

“Really, it’s to come to a final recommendation about how the church will relate to Girl Scouts of the USA,” he said.