The Obama administration’s new rule for faith-based partnerships has drawn various reactions: one observer warned they could cause problems for partnering religious groups, while another said the action also strengthens these groups’ protections against government abuse.

H. James Towey, the president of Ave Maria University, was a strong critic of the new rules.

“They will seek to secularize all faith-based providers that want to play ball with the government,” he told CNA.

Towey directed the White House Office of Faith-Based and Community Initiatives from 2002 to 2006, under President George W. Bush. He said the rules would have a “chilling effect” on organizations that “really care about the souls of the people they serve.”

Melissa Rogers, special assistant to the president and executive director of the White House Faith-based Neighborhood Partnerships, summarized the new federal rule in a March 31 statement.

The rule applies to nine federal departments, and aims to clarify that faith-based organizations are eligible to take part in federally funded programs “on the same basis as any other private organization.” All decisions of federal funding to faith-based organizations must be based “solely on merit” and “free from political interference, or the appearance of such interference.”

The rule also aims to clarify that “explicitly religious activities” cannot be supported with direct financial assistance. The organization must separate privately funded religious activities from federally funded activities.

The rule bars faith-based organizations that receive federal assistance from discriminating against beneficiaries based on “religion, a religious belief, a refusal to hold a religious belief, or a refusal to attend or participate in a religious practice.” The rule requires these faith-based organizations to notify beneficiaries of these protections.

Towey said the rule should be read in a broader political context.

“If this were all they have done, you could hope to take them at face value. But this is part of an eight-year campaign,” he said. “They drove the bishops’ conference out of refugee resettlement. They attempted to get faith-based organizations into the business of promoting abortion if they wanted to resettle refugees. This has been a drumbeat out of the Obama administration.”

In early 2011, political appointees at the Department of Health and Human Services’ Office issued instructions indicating there would be a “strong preference” for grants to organizations that refer for the “full range of legally permissible gynecological and obstetric care.” The U.S. bishops’ program would not refer for abortions and other procedures and drugs that violate Catholic ethics.

Later that year the federal government declined to renew a $19 million grant to the U.S. bishops’ program for human trafficking victims. Political appointees at the Department of Health and Human Services decided against the grant, though the department staff had recommended the grant renewal based on the scores of an independent review board.

The rule change has other consequences. Beneficiaries must be told that they can report rule violations to the federal agency or intermediary in charge of the program. If a beneficiary or potential beneficiary who objects to a funded organization’s religious character, the organization must take “reasonable efforts” to refer them to an alternative provider.

In Towey’s view, the new rule could easily be abused.

“If you’re a faith-based group, you’re now wondering is it worth partnering with the government and having these handcuffs on.”

“Faith-based groups knew where the lines and boundaries were. But there wasn’t bureaucratic red tape,” Towey added.

Brian W. Walsh, a religious freedom advocate who is the president of Civil Rights Research Center, was more positive about the rule.

He told CNA that the new regulations “reaffirm a large majority of the even-handed standards for faith-based partnerships that were established by both the Clinton and second Bush administrations.”

“The rules help prevent federal agency demands that faith-based partners deny their religious identity simply because they are using federal grants to care for the needy,” he said. “Partners need not, for example, purge their facilities of all religious symbols.”

The rules also protect faith-based organizations’ rights to hire staff who adhere to their religion. However, Walsh noted that federal rules already allow a needy person with federal benefits support to choose a service provider.

“It is therefore questionable why the rules open the door for a recipient to pick and choose which portions of a faith-based provider’s program he does not want to participate in,” he said.

Stanley Carlson-Thies of the Institutional Religious Freedom Alliance said the rule was positive, though he saw cause for concern in the rule’s new regulations for programs that receive indirect funding.

In an April 4 commentary at the Institutional Religious Freedom Alliance, he said that previous regulations forbade religious discrimination against beneficiaries. The new rule expands this regulation to programs that receive indirect funding, such as a federal voucher for a job training program.

If any parts of such a program are framed and taught from a specifically religious perspective, a beneficiary must be allowed to opt out of these portions even if they are considered integral to the program.

Carlson-Thies, who served at the White House Office of Faith Based & Community Initiatives from 2001-2002, also served on a task force under President Obama to draft recommendations on how to clarify church-state rules and federal funding.

The new rule becomes effective 30 days after April 4, while recipients of federal funding have 90 days after April 4 to comply. The rule is intended to implement a Nov. 17, 2010 executive order from Obama.

That executive order explicitly allowed groups that receive federal funding to display religious iconography in their facilities, maintain religious references in the names of their programs, choose board members on the basis of their religion, and make reference to faith in their mission statements and internal documents.

CNA sought comment from Catholic Charities USA, which was not able to comment as it was in the process of reviewing the regulations and their impact on its agencies.