A contentious battle between Catholic groups and the Obama administration has flared in recent days, fueled by the new health-care law and ongoing divisions over access to abortion and birth control.

The latest dispute centers on a decision by the Department of Health and Human Services in late September to end funding to the U.S. Conference of Catholic Bishops to help victims of human trafficking, or modern-day slavery. The church group had overseen nationwide services to victims since 2006 but was denied a new grant in favor of three other groups.

The bishops organization, in line with the church’s teachings, had refused to refer trafficking victims for contraceptives or abortion. The American Civil Liberties Union sued, and HHS officials said they made a policy decision to award the grants to agencies that would refer women for those services.

The bishops conference is threatening legal action and accusing the administration of anti-Catholic bias, which HHS officials deny.

The fight further sours an already difficult relationship between the government and some Catholics over several issues. The bishops fiercely oppose the administration’s decision in February to no longer defend the federal law barring the recognition of same-sex marriage. Dozens of Catholic groups also have objected in recent weeks to a proposed HHS mandate — issued under the health-care law — that would require private insurers to provide women with contraceptives without charge.

Health and Human Services Secretary Kathleen Sebelius. (Charles Dharapak/AP)

On the trafficking contract, senior political appointees at HHS awarded the new grants to the bishops’ competitors despite a recommendation from career staffers that the bishops be funded based on scores by an independent review board, according to federal officials and internal HHS documents.

That prompted a protest from some HHS staffers, who said the process was unfair and politicized, individuals familiar with the matter said. Their concerns have been reported to the HHS inspector general’s office.

Under HHS policies, career officials usually oversee grant competitions, and priority consideration is given to the review board’s judgment. The policies do not prohibit political appointees from getting involved. “I think it’s a sad ma­nipu­la­tion of a process to promote a pro-abortion agenda,” said Sister Mary Ann Walsh, a spokeswoman for the conference. She has written on the organization’s blog that the decision reflects an HHS philosophy of “ABC (Anybody But Catholics)’’.

HHS denies bias

HHS officials denied any bias and pointed out that Catholic groups have received at least $800 million in HHS funding to provide social services since the mid-1990s, including $348 million to the bishops conference. One of those grants, $19 million to aid foreign refugees in America, was awarded to the bishops three days after the anti-trafficking contract expired Oct. 10.

“There wasn’t an intention to go out and target anybody,’’ said George Sheldon, acting assistant secretary for HHS’s Administration for Children and Families. “Nobody has ownership of a contract.’’ He added that the agency “followed standard procedure.”

HHS had said that at least four grants for trafficking victims would be awarded, but Sheldon said he decided that the $4.5 million would be shared among three nonprofit groups: Heartland Human Care Services, Tapestri and the U.S. Committee for Refugees and Immigrants.

The applications of Tapestri and the U.S. Committee for Refugees and Immigrants were scored significantly below the Catholic bishops’ application by the review panel, the individuals familiar with the matter said.

“I don’t think there was any undue influence exerted to make this grant go one way or another,’’ Sheldon said. “Ultimately, I felt it was my responsibility — and I’m not trying to get anyone off the hook here — to do what I thought was in the best interests of these victims.’’

The dispute marks the latest chapter in HHS Secretary Kathleen Sebelius’s complicated relationship with the church. Raised Roman Catholic in Ohio, she was fiercely criticized by Catholic and other groups when she was governor of Kansas because she vetoed bills that would have imposed new restrictions on abortion providers. At one point, the archbishop of Kansas City asked her to stop taking Communion.

On Aug. 1, HHS issued a proposed mandate that would require insurers to provide contraceptives and other preventive health services for women in employee coverage, a decision hailed by Democrats and women’s groups but opposed by Catholic groups and social conservatives. Catholics argue that a proposed exemption for some religious employers is far too narrow.

A dispute over abortion

The trafficking contract was aimed at providing housing, counseling and other services to trafficking victims who are held in workplaces through force or fraud. It was first awarded in 2006, after a controversial decision by the George W. Bush administration to direct more federal social service contracts to faith-based groups. The contract ultimately provided the Catholic bishops with more than $19 million to oversee those services.

At the time, several members of the federal review board assessing the bidders raised concerns that the Catholic group would not refer victims for abortions or contraceptives, according to documents in the ACLU lawsuit. The documents said the board still ranked the Catholic group far above other applicants.

The ACLU, in the lawsuit it filed in U.S. District Court in Boston in 2009, argued that many women are raped by their traffickers and don’t speak English, making it hard for them to find reproductive services without help.

While the bishops’ organization would not refer women directly, it allowed subcontractors to arrange for the services, but it refused to reimburse the subcontractors with federal dollars.

“The principle of church teaching is that all sexual encounters be open to life,’’ said Walsh, of the bishops conference. “It’s not a minor matter; this is intrinsic to our Catholic beliefs.’’

The ACLU lawsuit argued that HHS allowed the Catholic group to impose its beliefs. But in defending the contract on behalf of HHS, Justice Department lawyers argued that the contract was constitutional and that the bishops had been “resoundingly successful in increasing assistance to victims of human trafficking.’’

This spring, as the contract approached its expiration, HHS political appointees became involved in reshaping the request for proposals, adding a “strong preference” for applicants offering referrals for family planning and the “full range” of “gynecological and obstetric care.’’ That would include abortions and birth control; federal funds cannot be used for abortions, except in cases of rape, incest or danger to the life of the mother.

“When important issues that are a priority arise, it’s common for senior policy advisers of the department to have a dialogue . . . to reach the best policy decision,’’ said Sharon Parrott, a top Sebelius aide closely involved in the process. “The priority in this case was how to best meet the needs of victims of trafficking so they can take control of their own lives.’’

The “strong preference” language now lies at the heart of the dispute. Sheldon, the HHS assistant secretary, said that it played a role in selecting the new grantees and that “it’s very important that these victims, who have experienced trauma . . . be provided the full range of information.’’

The bishops conference says the language essentially stacked the deck against the group and violated federal laws barring discrimination based on religion. “This was a political decision,’’ Walsh said.