PARMA, Ohio (RNS) Sister Mary Ann Flannery is under investigation. So is Sister Pat Rogers.

And all the other Catholic nuns living in the United States.

Yet the two sweeping investigations by the Vatican are being conducted so quietly that the nuns themselves are not sure what the inquiries are all about.

“We can’t figure out why this is happening,” said Flannery, director of the Jesuit retreat house in Parma. “We’re just doing our jobs.”

One investigation, known as an “apostolic visitation” to “look into the quality of life” in sisters’ religious communities, began last December.

The other inquiry, launched last spring, targets the Leadership Conference of Women Religious (LCWR), an umbrella group that represents 95 percent of the nation’s 59,000 nuns.

Both investigations have raised questions and speculation.

“What do they mean by `quality of life?”‘ asked Rogers, a nun for 60 years who is now retired from teaching and civic work. “We think we have done very well with living our lives.”

The visitation was ordered by Cardinal Franc Rode, who oversees religious orders for the Vatican. Rode appointed Mother Mary Clare Millea, superior of the Connecticut-based Apostles of the Sacred Heart of Jesus, to carry out the inquiry. Millea has begun sending teams of investigators to interview mothers superior.

Those investigative reports are to be kept confidential and sent to Rode. The nuns will not be allowed to see them.

“It’s ludicrous,” said Sister Jane Pank, who runs a program that finds housing for seniors and for women and children coming out of shelters. “Everything is secret and we won’t know what’s in the report. So what’s the point?”

Critics of the investigations believe the Vatican is trying to rein in U.S. nuns seen as too independent and generally open-minded about hot-button issues like ordaining women, gay marriage and contraception.

Church officials involved with the probe did not respond to a request for comment.

Many American nuns embraced the church’s Second Vatican Council, which, more than 40 years ago, opened the gates of social activism, freedom of expression and conscience and proclaimed a respect for all religions.

With Vatican II, nuns shed their habits, rolled up their sleeves and went to work helping the poor, the elderly and the sick. Many of them left convents to live independently and work in social and political grassroots programs.

“The sisters in the U.S. are quite different from sisters in other parts of the world,” said the Rev. Thomas Reese, a Jesuit theologian at Georgetown University in Washington. “They are highly educated, they run multimillion-dollar hospitals and universities and they feel they should make their own decisions about their lives and their communities.

“Sisters elsewhere in the world are not that educated. They say, `Yes, Father,’ and do what they’re told. The Vatican doesn’t know how to deal with educated women who are smart and ask questions.”

According to its Web site, visitation investigators have been asking mothers superior a host of questions about their orders, including: “What is the process for responding to sisters who dissent publicly from church teaching and discipline?”

“That’s the dynamite,” said Reese. “They’re looking for a way to bring the sisters and all Catholics in the United States in line with Vatican teachings. Good luck. The more they try to do it, the more angry and alienated people get.”

The investigation of the LCWR is headed by Bishop Leonard Blair of Toledo, Ohio. He declined to be interviewed for this story.

Officials at LCWR headquarters in Silver Spring, Md., also declined to discuss the investigation. But the organization, released a statement after its August convention that was critical of the inquiry.

“Among expressed concerns are a lack of full disclosure about the motivation and funding sources for the studies,” the statement said. “The leaders also object to the fact that their orders will not be permitted to see the investigative reports about them that are being submitted directly to the Vatican.”

Last April, the LCWR sent letters to its members informing them of the investigation and outlining some of the details. The letter noted that the Vatican’s Congregation for the Doctrine of Faith, headed by Cardinal William Levada, had asked LCWR leaders back in 2001 what initiatives they were taking to promote official church teachings.

Levada, the former archbishop of San Francisco, was primarily concerned about the nuns’ positions on three issues: a male-only priesthood; the centrality of Jesus and the Catholic Church in salvation; and “the problem of homosexuality.”

The LCWR’s April letter indicated that Levada had said he was not satisfied with the nuns’ answers. As a result, Levada said, it was necessary to launch “a doctrinal assessment of the activities and initiatives” of the LCWR.

But to many nuns, the assessment is more of an inquisition, questioning their Christian faith. Pank, for one, called it “arrogant.” Reese, from Georgetown, seemed to agree.

“Considering all the great works they’ve done in this country, it’s kind of ridiculous they’re under this investigation,” he said. “The Catholic Church was built on the slave labor of these sisters. We should be supporting them as much as we can.”

(Michael O’Malley writes for The Plain Dealer in Cleveland)