* Vatican aims to rein in conference of Catholic nuns

* Differences over ordination of women, ministry to gays

* Some U.S. nuns have long challenged Catholic doctrine

By Stephanie Simon

April 20 (Reuters) - When Pope John Paul II arrived in the United States in 1979, the president of the nation's most powerful organization of nuns met him with a challenge.

In a bold welcoming address, Sister Theresa Kane called on the pope to include women "in all ministries of our church," including the priesthood. The pope sat silent, his expression stony.

That moment did not change Vatican policy.

But it unveiled growing tensions between the Vatican and American nuns. The conflict would continue to mount for the next three decades, until this week the Vatican finally moved to reassert control over the aging but still ferociously independent conference of Catholic sisters.

In a stinging "doctrinal assessment," the Vatican accused the Leadership Conference of Women Religious - an umbrella group representing most American nuns - of numerous grave breaches of doctrine and decorum.

The report, four years in the making, found that the nuns promoted political views at odds with those expressed by U.S. Roman Catholic bishops, "who are the church's authentic teachers of faith and morals." The Vatican chastised the nuns for airing discussions about the ordination of women, the church patriarchy and ministry to gay people.

The Vatican also rebuked the nuns for spending too much time "promoting issues of social justice" while failing to speak out often enough about "issues of crucial importance to the life of the church and society," such as abortion and gay marriage.

Determined to cleanse the sisterhood of "radical feminist themes incompatible with the Catholic faith," the Vatican appointed Archbishop J. Peter Sartain of Seattle to effectively take control of the Leadership Conference, rewriting its statutes, supervising its meetings, and investigating its relationships with politically active groups.

Officials of the nuns' leadership conference said they were "stunned" by the crackdown. But Catholics who have studied the growing rift between the church hierarchy and American nuns said it was a long time coming.

'BREWING FOR 40 YEARS'

"This has been brewing for 40 years," said Ann Carey, the author of the book "Sisters in Crisis: The Tragic Unraveling of Women's Religious Communities."

Many U.S. women's religious orders began moving away from traditional roles - and their traditional deference to the Vatican - in the early 1970s after the Second Vatican Council, a conclave dedicated to modernizing Catholic religious life, Carey said.

Some stopped wearing the traditional garb known as habits. Some left the teaching and nursing professions to take up grittier work running soup kitchens or homeless shelters. Some moved out of convents to live on their own.

Some even directly defied Catholic doctrine. Donna Quinn, a Chicago nun who calls herself "a feminist and an activist and proud of it," spent years escorting women through a gauntlet of protesters to a health clinic that provided abortions. She has repeatedly called on the Vatican to reconsider its opposition to contraception and abortion - and she says she will not let any bishop silence her now.

"The institutional church men forget that we are women who are educated, articulate, seekers of truth and very, very holy," said Quinn, the coordinator of an outspoken group called the National Coalition of American Nuns.

The nuns' activism and defiance of church doctrine has long angered conservative Catholics. Several orders of nuns left the Leadership Conference to start their own, more traditionalist group. The Vatican, meanwhile, repeatedly signaled and issued at least one formal warning that American nuns must return to the fold.

'SECULAR FEMINISM'

"The attitudes and values of secular feminism had entered into their mindset" and created an "unhealthy" movement, said Russell Shaw, a church historian, author and former spokesman for the U.S. Conference of Catholic Bishops.

But the nuns were not inclined to back down.

Sister Joan Chittister, a former president of the nuns' leadership conference, said the nuns saw themselves as helping, not hurting, the church. Their difficult questions must be asked, she said, if the church is to remain vibrant, relevant and respected. "When you begin to suppress that, it's immoral," Chittister said. "It's a mistake for the church. And it's despair for its people."

The nuns' motto, declared on their website: "We risk being agents of change within church and society."

Fed up, the Vatican in 2008 launched its "doctrinal assessment" of the conference. It also completed a separate investigation of the quality of life for American nuns, but that report has not been made public.

Sister Simone Campbell, who runs a Washington-based Catholic social justice group called Network, said she believed the Vatican's harsh tone stemmed from anger about the nuns' support for President Barack Obama's efforts to get a healthcare overhaul through the U.S. Congress in 2009 and 2010. U.S. bishops opposed the law, signed by Obama in 2010.

The Vatican "clearly got upset that we were effective at communicating our views politically," Campbell said.

The nuns are not always at odds with the Vatican or U.S. bishops.

Last week, for instance, Campbell joined other nuns and theologians in calling on the bishops to speak out against Republican proposals for the federal budget. The bishops did so, protesting that the budget blueprint violated moral principles by slashing programs for the poor while protecting the wealthy. The nuns have also worked with the bishops on immigration reform.

But the nuns' Leadership Conference has not expended much energy on other priorities the bishops hold dear, like working to end abortion and gay marriage. The Vatican report said that was unacceptable.

For the most part, nuns did not actively oppose bishops on these issues - "it just was not part of their agenda," said the Reverend Thomas Reese, a senior fellow at the Woodstock Theological Center at Georgetown University, a Catholic university in Washington. "In a sense, they're being indicted for being silent."

The nuns' Leadership Conference has not yet decided how to respond to the Vatican's rebuke. But some Catholic scholars suggest that the issue will soon be moot.

The generation of nuns that struck out so brazenly in the early 1970s is aging. There are more nuns over age 90 than there are under age 60, according to the Center for Applied Research in the Apostolate at Georgetown University.

In 1975, the United States had more than 135,000 nuns. Now, there are fewer than 56,000.

In recent years, some religious orders have reported a recruiting uptick. But young novices are flocking not to the fiercely independent religious orders that so irk the Vatican but to more traditional orders - those that wear habits, live together in a convent, devote themselves to teaching, nursing and prayer, Georgetown researchers found.

Given that the younger nuns tend to be more traditional, church historian Shaw said he did not think the Vatican should expend too much effort reining in the older generation.

"Look at their median age," Shaw said. "This is an issue that is going to be settled by actuarial tables, not theologians or canon lawyers."

Sister Quinn of Chicago disagreed. "There's an old, old saying," she said, "that you cannot put the toothpaste back in the tube." (Reporting by Stephanie Simon in Denver; Editing by Marilyn W. Thompson and Will Dunham)