(RNS) Relations between the Vatican and the American nuns who are under investigation seem to be worsening after the sisters said Monday (June 18) that initial discussions with Rome about a resolution to their standoff were “difficult” and that comments by several U.S. bishops have not made negotiations easier.

The statement by the board of the Leadership Conference of Women Religious, as well as subsequent remarks by the nun who heads the LCWR, may herald a longer and broader struggle inside the church.

“We have never considered ourselves in any way unfaithful to the church, but if questioning is interpreted as defiance, that puts us in a very difficult position,” Sister Pat Farrell, head of the LCWR, said in an interview with the National Catholic Reporter on Monday.

Farrell said that “together with people around the country who have been supportive of us, our desire is to do what we can, for their sake and for ours, to help create a safe and respectful environment, where together with church leaders we can raise questions openly and search for truth freely, addressing some of the complex issues of our times.”

But Farrell added that such questioning “can only take place in a climate of mutual trust.”

She said that lack of trust was evident on June 12 when Farrell and the LCWR's executive director, Sister Janet Mock, met with Cardinal William Levada, the American who heads the Vatican's doctrinal office and who is overseeing an overhaul of the LCWR.

In April, the Vatican announced that Pope Benedict XVI had authorized a takeover of the LCWR, which represents about 80 percent of the nation’s 57,000 nuns and sisters. The Vatican's "doctrinal assessment" said the group was not sufficiently promoting orthodox teachings on sexuality and gender and was spending too much time focusing on social justice issues.

Although the Vatican has been officially scrutinizing the LCWR for several years – and has viewed the U.S. nuns with some suspicion for decades – the takeover came as a surprise. LCWR leaders requested a face-to-face meeting with Levada, head of the Congregation for the Doctrine of the Faith, and Seattle Archbishop Peter Sartain, who Benedict named to direct the Vatican effort.

After last week’s talks in Rome, Farrell and Mock said the meeting had been an opportunity for “open dialogue.” A Vatican spokesman said the meeting took place “in an atmosphere of openness and cordiality.”

But right after the meeting, Levada gave an interview in which he said the talks may in fact be a “dialogue of the deaf,” and said the nuns are associating with people who “aren't representing the church with any reasonable sense of product identity.” Sartain and another U.S. bishop involved in the takeover also said the investigation was aimed at the LCWR, not nuns in general.

Farrell called Levada’s comment “unfortunate” and in its statement on Monday, the LCWR rejected efforts to try to separate the group from the wider community of U.S. nuns, which it said has “keenly felt” the impact of the Vatican campaign.

LCWR also said the outpouring of support for the nuns was evidence that the conflict has struck a chord as “many others are also concerned about how to live as people of faith in the complexities of these times.”

“The concerns they have shared with LCWR will be part of the conference’s discernment of its response” to the Vatican, it said.

The LCWR holds its annual assembly in St. Louis in August, during which the entire membership will discuss the next steps to take.