The Vatican says the probe, or "apostolic visitation," is to address issues such as declining membership in women's religious orders.
But it has provoked an uproar among some Catholics who admire the nuns and believe the visitation is an effort by conservatives to rein in sisters they believe have become too liberal.
This week, in addition to Murphy's column, bishops in California issued a statement supporting the nuns there, while the Vatican cardinal in charge of the visitation issued a letter defending it.
"The fact [Rome] felt compelled to put out some kind of statement is one indication that there is a pushback," said John Allen, Rome correspondent for The National Catholic Reporter.
New York Archbishop Timothy Dolan, in a blog, wrote that the visitation "is well worth discussing, and hardly exempt from legitimate questioning."
Murphy's column in this week's Long Island Catholic offers a nuanced view of the effort. Murphy, of the Diocese of Rockville Centre, writes that visitations are a means to improve aspects of the Church and notes that the seminary in Huntington had one in 2001 shortly after he took over here as bishop.
But, he also takes great pains in the column to laud the nuns here.
"The key to understanding this visitation is respect," Murphy wrote. "These sisters deserve and must always have our respect, the respect of the Holy See and the Visitation Committee, the respect of the entire Church. Their dignity must never be compromised, and their commitment to a vowed life of consecration to God always honored."
Margaret O'Brien Steinfels, co-director of the Fordham Center on Religion and Culture, said Murphy's comments were similar to those by the California bishops in that "it's fine-tuned.
On the one hand expressing gratitude" to the sisters, but "none of them really raise, on the face of it, an objection to having the visitation go on."
Still, she called it "a very unusual fact" that Murphy wrote that "the whole project was outside the hands of the U.S. bishops."
With the exception of cloistered nuns, all 59,000 sisters in the United States are subject to the Vatican probe, which does not include nuns in any other country.
About 2,000 sisters work on Long Island, and their ranks have steadily dropped since the mid-1960s.
Rome says the visitation also will look at the sisters' prayer life and "fidelity to the Church's teachings."
The visitation began this year with letters sent in January to religious orders.
In September they received questionnaires, and next year some will receive on-site visits.
A report is due for the Vatican in 2011 but will be kept confidential.
Some conservative Catholics welcome the visitation and hope it may herald a return to a more traditional life of habits, convents and sisters going to Mass together.
"I see it as something very positive," said Sister Margaret Regina of the Little Sisters of the Poor based in Queens Village. Her order still dresses traditionally, and she said four new members "really love the habit."
But Steinfels said that "certainly lots of lay people . . . were totally amazed that someone in the Vatican could decide to send someone to, in effect, investigate - even if they use the word 'visitation' - American nuns. Despite all the problems of the Church, they remain beloved by most lay Catholics."
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