Despite a compromise allowing conservative church-sponsored units to pick their own volunteer leaders, the Mormon church said it might leave the organization after Monday’s decision to lift a nationwide ban on openly gay adult leaders.

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The Boy Scouts of America on Monday ended its nationwide ban on openly gay adult leaders. But despite a compromise allowing conservative church-sponsored units to pick their own volunteer leaders, the Mormon church, the country’s largest sponsor of Scout units, said it might leave the organization.

“The Church of Jesus Christ of Latter-day Saints is deeply troubled by today’s vote by the Boy Scouts of America National Executive Board,” said a statement issued by the Mormon church moments after the Scouts announced the new policy.

“In spite of a request to delay the vote, it was scheduled at a time in July when members of the Church’s governing councils are out of their offices and do not meet. When the leadership of the Church resumes its regular schedule of meetings in August, the century-long association with Scouting will need to be examined,” the statement said.

Mormons use the Boy Scouts as their main nonreligious activity for boys, and the Cub Scout and Boy Scout units they sponsor accounted for 17 percent of all youths in Scouting in 2013, the last year for which data have been published.

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The negative reaction to Monday’s vote took many Boy Scout leaders by surprise; it had been widely assumed that the exemption for religious sponsors would keep them in the fold.

“The church has always welcomed all boys to its Scouting units regardless of sexual orientation,” the statement by the church headquarters continued. “However, the admission of openly gay leaders is inconsistent with the doctrines of the church and what have traditionally been the values of the Boy Scouts of America.”

Under the Boy Scout policy adopted Monday, discrimination based on sexual orientation will also be barred in all Boy Scout offices and for all paid jobs — a step that could head off looming lawsuits in New York, Colorado and other states that prohibit such discrimination in employment.

One legal threat was immediately averted. In response to the change, the New York state attorney general, Eric T. Schneiderman, announced Monday that his office was ending its investigation of the Scouts for violating state anti-discrimination laws.

To avoid the wholesale defection of conservative religious groups, the Boy Scouts said church-based local units would remain free to exclude gay adults from voluntary leadership roles like scoutmasters and Cub Scout den and pack leaders.

The Boy Scouts’ national executive board, composed of about 71 civic, corporate and church leaders, adopted the changes with 79 percent of those who participated in a telephone meeting voting in favor, according to an announcement issued by the Scouts.

The announcement did not say how many board members were not present.

Many Scouting leaders said they had not expected the Mormon church’s sharp response and threat to leave.

“My assumption was that the concept voted on today had been fully vetted so as to avoid any unnecessary surprises,” said Jay Lenrow, a longtime volunteer Scout leader in Baltimore who is on the executive committee of the Scouts’ Northeast region and serves on the organization’s national religious relationships committee.

“I can only say that I’m hopeful that when the leadership of the LDS church meets and discusses the issue, that they will find a way to continue to support Scouting.”

The policy change was widely seen as a watershed for an institution that has faced growing turmoil over its stance toward gay people, even as it struggles to halt a long-term decline in members.