The pope's personal representative to the United States said Wednesday the Catholic Church in America is living in a "particularly challenging period of its history."
His words underscored the issues being tackled by the U.S. Conference of Catholic Bishops, which is holding its spring General Assembly in Atlanta.
The gathering of the nation's top Catholic leaders included discussions of government threats to religious liberties and sexual abuse by clergy.
"Of course, I am thinking of the whole question of freedom of religion and of conscience issues close to the heart of the American people -- and of the indispensable role of the bishop as chief shepherd in his diocese and all of this in the context of an election year, making interventions even more delicate," said Archbishop Carlo Vigano, the pope's representative to the U.S.
High on the agenda was the Obama administration's mandate that health insurers and employers provide a wide range of contraceptive coverage for employees. The church claims that it violates religious liberty and moral conscience.
Although the administration says religious-affiliated institutions such as schools and hospitals do not have to pay for or refer employees for such coverage, the church argues that since most dioceses are self-insured, they would still bear that responsibility. Their affiliates would also be part of that self-insured plan.
It's a question "of change in the long-standing respect that the government has for religious freedom," said Atlanta Archbishop Wilton D. Gregory.
Churches, synagogues, mosques and religious organizations have not previously "been forced by government edict to violate their conscience vis-a-vis ethic or moral issues," he said.
It should be of "serious interest" to non-Catholics too, he added.
"If the government can force Catholics to do something on Tuesday, then the Methodists better be worried about what's going to be coming down the line on Thursday that would be in violation of their religious freedom," he said.
Bishops insisted they had no partisan agenda. They said they were forced into action by state and federal policies that they say would require them to violate their beliefs in order to maintain the vast public-service network the church has built over a century or longer.
"It is not about parties, candidates or elections as others have suggested," said Baltimore Archbishop William Lori, chairman of the bishops' religious liberty committee. "The government chose to pick a fight with us."
The bishops are organizing a "Fortnight for Freedom," two weeks of rallies and prayer services on religious freedom leading up to the Fourth of July. Vigano told the bishops that the advocacy effort "has my full support."
The bishops also received an update on how the church is addressing the priest sex abuse scandal. Al Notzon III, chairman of the bishops' national review board, said that while there have been major strides and transparency, it's still "an evolving process."
Notzon said the problem has moved beyond being a legal issue and become more of a pastoral issue that involves training, constant monitoring of the effectiveness of programs, clergy evaluations, help for victims and the restoration of trust among parishioners.
While thousands of victims have come forward, he conceded it was "impossible to know the number of victims."
Meanwhile, more than a dozen people gathered outside the hotel to protest the meeting.
The group spoke out against the Vatican's recent criticism of members of the Leadership Conference of Women Religious, which represents many of the nation's nuns, for being "incompatible with the Catholic faith." The group said it had a petition containing more than 57,000 signatures.
"I think the nuns do an incredible job of reflective discernment about what is God's call for them," said Natallie Keiser, who wore a button reading "I Stand with the Sisters."
"The bishops need to respect them trying to help the poor and the marginalized and not control it."