By Dan Gilgoff, CNN.com Religion Editor

(CNN) - The Vatican denies there's a connection, but its reprimand of an influential American nun, at a moment when the Holy See is already engaged in an intense fight with most American nuns, sends a clear message: The Catholic Church’s leaders think America’s nuns have gone rogue and must be reined in.

The Vatican on Monday censured Sister Margaret A. Farley, who teaches at Yale Divinity School, over a 2006 book she wrote that the church said is out of step with official church teaching on human sexuality.

Just weeks before, the Vatican issued a major report condemning the groups that represent most American nuns, saying those organizations had promoted “radical feminism” while neglecting teachings against homosexuality and abortion.

“The Vatican believes that there is a climate of dissent in some quarters of the women’s religious life in America,” said John Allen, CNN’s Vatican analyst. “They are trying to deal with that, and both these developments speak to that.”

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In its reprimand of Farley, the church focused on her book “Just Love: A Framework for Christian Sexual Ethics,” which it said condones masturbation and homosexuality.

“Masturbation is an intrinsically and gravely disordered action,” the church said in a statement Monday that characterized “homosexual acts” as “acts of grave depravity.”

The reprimand warned church officials not to use Farley’s book, raising eyebrows in Catholic circles because she is one of the country’s most respected female Catholic theologians.

The Rev. Brian Linnane, a Jesuit priest and president of Loyola University Maryland, did his doctoral work in theology under Farley. He said the notification could have a chilling effect on academic freedom at Catholic institutions.

“There’s a sense that the vocation of the theologian is diminished in this notification to where it’s just, ‘Keep repeating what we’ve already said and don’t question it, don’t critique it, don’t try to help us make it more adequate.’ And I think that’s troubling,” he said.

Linnane said people who read the book knew that Farley was departing from Catholic teaching in certain areas.

“She did not write a book about sexual practices. She wrote a new framework to think about sexual ethics, which looks at justice, instead of procreation or abstinence, which have been part of the tradition,” he said.

“I don’t think it’s a question of right or wrong so much as I think it is of the ability to raise critical questions, to try and develop new understandings of the theological tradition and in this case of the moral tradition.”

Linnane said the Vatican is right to be sure that public ministers such as priests and nuns be on the same page doctrinally as the church leaders, and he noted the rebuke was specifically against the book, not the author.

“There’s no silencing of Sister Farley in the notification, there’s no threat to her membership in her religious community; it’s just about the book, which everyone agrees probably shouldn’t be taught in Catholic seminaries, certainly shouldn’t be taught in religious education classes for young persons. Everyone agrees it’s theological speculation,” he said.



The censure came days after the leadership that represents most American nuns concluded a meeting in Washington to devise a response to an April Vatican assessment that accused the nuns of hosting speakers who preached “radical feminism” at an annual gathering of the Leadership Conference of Women Religious. The group represents about 80% of American nuns.

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The report also said the nuns were too focused on social justice and not enough on opposing abortion, euthanasia and same-sex marriage.

The recent reprimands come about a year after U.S. Catholic bishops rebuked another nun, Sister Elizabeth Johnson at Fordham University, for her writings.

The bishops said that Johnson falsely claims the Catholic Church’s names are “metaphors that do not apply to the reality of God within the traditional Catholic understanding.”

“In the last 12 months you’ve seen two of America’s leading Catholic nuns who are theologians in the cross hairs,” Allen said. “I’m not sure there’s anyone left of their stature to go after.”

Many parts of the American nuns’ community and the Catholic academic world have come out swinging against the Vatican critiques. In a statement, Farley defended her work, saying it was not meant as an official church teaching.

Farley said she feared the Vatican “misrepresents (perhaps unwittingly) the aims of my work and the nature of it as a proposal that might be in service of, not against, the church and its faithful people.”

On Friday, the leaders of the American nuns whom the Vatican had criticized said the Holy See’s report was “based on unsubstantiated accusations and (was) the result of a flawed process that lacked transparency” and that the report had “caused scandal and pain throughout the church community.”

Representatives of the Leadership Conference of Women Religious are flying to Rome this week to try to chart a course forward with Vatican officials. Church experts said that the nuns could accept the assessment, negotiate or resign en masse and form a new group outside the watchful eye of the Vatican.

The reprimands originate from the Vatican’s powerful Congregation for the Doctrine of the Faith, which Pope Benedict XVI led for decades before his elevation to the papacy.

In interviews conducted while he held that earlier post, Benedict spoke often about growing the church by pruning - becoming smaller but more devout before expanding.

It is hard to know what the reaction to the fight between American nuns and the Vatican is within the American Catholic community, but there have been some pockets of protest against the Vatican’s actions.

“It’s one thing when the Vatican goes after a theologian, because most rank-and-file Catholics don’t know any theologians,” Allen said. “But so many have been educated by sisters in a school, taken care of by a sister at a hospital or know a nun in their parish that is running the office."

He added, “When there’s a perception that sisters are under fire, there’s a tendency to support them.”

There is evidence that the reprimand against Farley has raised her profile as a theologian. Her "Just Love" was the best-selling religious studies book Tuesday on Amazon.com.

- CNN's Eric Marrapodi contributed to this report.