Sister Farley said in a June 4 statement that she feared that the notification "-- while clear in its conclusions -- 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."

"I do not dispute the judgment that some of the positions contained (in the book) are not in accord with current official Catholic teaching," she said. "In the end, I can only clarify that the book was not intended to be an expression of current official Catholic teaching, nor was it aimed specifically against the teaching. It is of a different genre altogether."

She said the book "offers contemporary interpretations of traditional meanings for the human body, gender and sexuality" and "was designed to help people, especially Christians but also others, to think through their questions about human sexuality."

Sister Farley, who taught at Yale University Divinity School from 1971 to 2007 and now serves as Gilbert L. Stark professor emerita of Christian ethics, is a past president of both the Catholic Theological Society of America and the Society of Christian Ethics.

The five-page Vatican notification says the congregation first wrote to Sister Farley about its concerns through her superior, the president of the Sisters of Mercy of the Americas, more than two years ago. Urged to "correct the unacceptable theses contained in her book," Sister Farley sent responses in 2010 and 2011 that "did not adequately clarify the (book's) grave problems," the congregation said.

Mercy Sister Pat McDermott, current president of the Sisters of Mercy of the Americas, expressed "profound regret" at the issuance of the notification and said the process initiated by the Vatican congregation "has been lengthy, arduous and extremely difficult."

Calling Sister Farley "an extraordinary teacher and pastoral minister who is deeply committed to the Gospel and the following of Jesus Christ," she added, "While being faithful to her own faith tradition and commitments, her sensitivity to the varied circumstances, realities and needs of her students is the context she consistently honors."

The Yale professor emerita also drew praise from Harold Attridge, a Catholic layman who is dean of Yale Divinity School, who said she "has inspired generations of students ... to take seriously the task of theological ethics by examining the logic of our moral judgments in the light of Scripture, tradition and human experience."

"In time, I suspect, those who react negatively to (her book) will come to appreciate the important contribution it makes to what must be our constant effort to examine the foundations of our moral life," he added.

The congregation cited five specific problem areas in "Just Love," published by Continuum:

-- Masturbation: Sister Farley's view that masturbation "usually does not raise any moral questions at all" and "actually serves relationships rather than hindering them" does not "conform to Catholic teaching ... that masturbation is an intrinsically and gravely disordered action," the notification said.

-- Homosexual acts: Sister Farley writes in the book that "same-sex relationships and activities can be justified according to the same sexual ethic as heterosexual relationships and activities." But the Vatican said "this opinion is not acceptable" because it fails to distinguish between persons with homosexual tendencies, who must be respected, and homosexual acts, which are "intrinsically disordered" and "contrary to the natural law."

-- Homosexual unions: Sister Farley says domestic partnerships, civil unions and same-sex marriage can "be important in transforming the hatred, rejection and stigmatization of gays and lesbians that is still being reinforced by teachings of 'unnatural' sex, disordered desire and dangerous love." But the Vatican said that position "is opposed to the teaching of the magisterium," which says that "respect for homosexual persons cannot lead in any way to approval of homosexual behavior or to legal recognition of homosexual unions."

"Legal recognition of homosexual unions or placing them on the same level as marriage would mean not only the approval of deviant behavior, with the consequence of making it a model in present-day society, but would also obscure basic values which belong to the common inheritance of humanity," the notification said, quoting the doctrinal congregation's 2003 document, "Considerations regarding proposals to give legal recognition to unions between homosexual persons."

-- Indissolubility of marriage: Sister Farley writes that "a marriage commitment is subject to release on the same ultimate grounds that any extremely serious, nearly unconditional, permanent commitment may cease to bind." But the congregation, quoting the Catechism of the Catholic Church, says love "cannot be an arrangement 'until further notice'" and marriage requires "an unbreakable union" between the spouses.

-- Divorce and remarriage: Although a "residual bond" exists between former spouses, it does not preclude remarriage "any more than the ongoing union between spouses after one of them has died prohibits a second marriage on the part of the one who still lives," Sister Farley writes in her book. But the Vatican congregation said such a view "contradicts Catholic teaching," noting that the catechism says those who remarry civilly after a valid first marriage "find themselves in a situation that objectively contravenes God's law" and cannot receive Communion "as long as this situation persists."

General problems surrounding Sister Farley's book include an incorrect understanding "of the role of the church's magisterium as the teaching authority of the bishops united with the successor of Peter" and "a defective understanding of the objective nature of the natural moral law," the notification said.

"In addressing various moral issues, Sister Farley either ignores the constant teaching of the magisterium or, where it is occasionally mentioned, treats it as one opinion among others," it added. "Such an attitude is in no way justified, even within the ecumenical perspective that she wishes to promote."

The congregation expressed "profound regret that a member of an institute of consecrated life ... affirms positions that are in direct contradiction with Catholic teaching in the field of sexual morality."

"Furthermore, the congregation wishes to encourage theologians to pursue the task of studying and teaching moral theology in full concord with the principles of Catholic doctrine," the notification added.

Sister Farley has been no stranger to controversy during her career as a Catholic theologian.

She was among two dozen U.S. women religious threatened with expulsion from their religious communities by the Vatican for signing on to an Oct. 7, 1984, ad in The New York Times arguing that Catholics should be free to hold a variety of views about abortion.

Archbishop Pio Laghi, then papal pro-nuncio to the United States, and now-retired Archbishop John R. Quinn of San Francisco withdrew as speakers at a 1985 meeting of the Leadership Conference of Women Religious because Sister Farley also was scheduled to speak.

Her case was resolved in 1986, when a Vatican representative announced that she and other signers had expressed "their adherence to the teaching of the church with regard to abortion." The Vatican termed Sister Farley's action a "retraction" but the nun and her Mercy superior said no retraction was involved.

In 2005, the Cardinal Newman Society protested her choice as a commencement speaker at St. Xavier University in Chicago, describing Sister Farley as "an outspoken dissenter from Catholic teaching on embryonic stem-cell research, sexual activity and homosexual 'marriage.'"

She received the John Courtney Murray Award for excellence in theology from the Catholic Theological Society of America in 1992 and won the 2008 Louisville Grawemeyer Award in Religion, presented by Louisville Presbyterian Theological Seminary, for "Just Love."

She also served as co-director of the All-Africa Conference: Sister to Sister, a project designed to empower African women to tackle the AIDS pandemic in their country.