As the world watched the Vatican for an announcement of a new leader for the Roman Catholic faithful, the White House quietly made a leadership appointment of its own on Wednesday, to the office responsible for outreach to religious organizations: Melissa Rogers will be the new director of the Office of Faith-Based and Neighborhood Partnerships.

In some ways, the appointment of Ms. Rogers, a scholar of church-state legal issues, signals a new focus for the office. Her predecessor, the Rev. Joshua DuBois, sent President Obama Bible passages each morning and was known for fostering discussions with religious leaders on how to approach broad social goals. Yet Reverend DuBois made little headway in clarifying the First Amendment issues facing the office, which has been controversial since President George W. Bush created it in 2001.

But in another sense, Ms. Rogers will be continuing a job Mr. Obama asked her to start in 2009, when she led a diverse advisory committee charged with recommending ways to overhaul the office. Mr. Obama signed an executive order codifying many of the proposals, most of which clarified the ground rules for religious organizations seeking government aid for social services, late in 2010.

“Melissa will work to advance the president’s vision by promoting partnerships that serve the common good in ways that respect church-state separation and religious freedom,” a White House official said. “Like President Obama, Melissa believes that government and religious organizations can partner to promote the common good, but that government should not promote religion or become excessively entangled with it.”

The agency, originally called the Office of Faith-Based and Community Initiatives, was best known for its mission in the Bush administration to help religious groups secure government grants to provide social services. Yet, as Ms. Rogers noted in a 2011 speech, such partnerships “long predate the Bush administration, and they will far outlast the Obama administration.”

She added, “Thus it’s necessary and prudent to ensure that these partnerships are as effective and constitutionally compliant as they can be.”

She has praised the Obama administration for making nonfinancial relationships a priority, arguing that they can be just as effective without prompting thorny constitutional issues.

Yet Ms. Rogers has been vocal about her disagreement with current policy on an important issue for civil libertarians: allowing religious organizations to hire based on religion for programs that receive federal money.

“While I believe religious organizations should have full freedom to make religious calls regarding jobs subsidized by tithes and offerings,” Ms. Rogers said, speaking to the Baptist Joint Committee in 2011, “when government-funded jobs are involved, I believe the calculus changes.”

“I believe the Obama administration should undo Bush policies that broke with that tradition” of equally opportunity for taxpayer-financed positions, she said.

Church-state separation advocates cheered her appointment. The Rev. Barry Lynn, head of Americans United for the Separation of Church and State, called her a “good choice,” with a “wealth of knowledge about the constitutional issues surrounding church-state relations and a reputation for thoughtfulness and patience.”

Ms. Rogers is the director of the Center for Religion and Public Affairs at Wake Forest University in Winston-Salem, N.C., and a senior fellow at the Brookings Institution. She has previously been an executive director of the Pew Forum on Religion and Public Life and a general counsel for the Joint Baptist Committee, and she was a co-author of a case book on religion and law.