WASHINGTON — Inside the State Department, the definition of human rights is up for debate.

Secretary of State Mike Pompeo, an evangelical Christian, created a commission last July to provide a new vision for human rights policy that would more closely align with the “nation’s founding principles” and uphold religious freedom as America’s most fundamental value.

Human rights scholars have criticized the panel, saying it is filled with conservatives intent on promoting views against abortion and marriage equality. Critics also warn the commission sidesteps the State Department’s internal bureau tasked with promoting human rights abroad.

And former agency officials caution that elevating the importance of religion could reverse the country’s longstanding belief that “all rights are created equal” — and embolden countries that persecute same-sex couples or deny women access to reproductive health services for religious reasons.

“There are those who would have preferred I didn’t do it, and are concerned about the answers that our foundational documents will provide,” Mr. Pompeo said of the commission last fall to a conservative women’s group at the Trump International Hotel in Washington. “I know where those rights came from. They came from our Lord.”

He added: “Indeed, for years under the last administration, fighting for religious freedom was just an afterthought. But President Trump, our administration, recognizes it as our country’s first freedom, and it’s found at the very top of the Bill of Rights, so we kind of got it right.”

The commission’s report is expected to be released in early July, and is tightly held among Mr. Pompeo’s top aides. Diplomats note the report could be a tool to advance Mr. Pompeo’s religious beliefs and political aspirations, while proving detrimental to preserving the rights of women and gay, lesbian, bisexual and transgender people abroad.

“This is about the only human right they seem to care about,” David Kramer, who was assistant secretary of state for the Bureau of Democracy, Human Rights and Labor in the George W. Bush Administration, said of the commission’s focus on religion. “It seems to be a play for political support domestically, that could rebound to our detriment in foreign policy.”

The panel’s recommendations come as America’s commitment to human rights faces skepticism from organizations like the United Nations. The peacekeeping body issued a resolution on Friday condemning police brutality and “systemic racism” against people of African descent. Diplomats had to drop specific references to the United States to gain passage.

In response to the resolution, Mr. Pompeo on Saturday said bodies like the U.N.’s Human Rights Council should “recognize the strengths of American democracy and urge authoritarian regimes around the world to model” America’s values. (The United States quit the council two years ago after accusing it of bias against Israel.)

Experts warn this type of criticism from Mr. Pompeo will hold less sway if the secretary’s Commission on Unalienable Rights produces a document prioritizing religion above all else. Such a document could also play into the hands of repressive governments like Saudi Arabia and Iran that seek to narrowly define human rights.

The State Department declined to comment on the questions regarding the commission.

Mr. Pompeo’s advisory panel has met five times. The meetings were public and have been minimally attended. Human rights advocates, former State Department officials and academics say they have been alarmed at what has taken place.

“The bottom line: The commission is poised to adversely shape U.S. foreign policy,” experts at Duke University wrote in a recent blog post detailing the panel’s work. In their analysis of the panel’s meetings, they noted that a “a general skepticism” toward international human rights pervaded committee discussions.

Many commission members, they note, believe there are too many human rights, including Mary Ann Glendon, the head of the commission, who has said “if everything is a right, then nothing is.”

If the commission’s report to Mr. Pompeo reflects the panel’s discussions to date, and makes a case to prioritize one human right over another, observers say it could upend diplomatic efforts to stop the Chinese persecution of the Uighur minority and promote women’s rights in places like Iran and Saudi Arabia.

“My hope is that this document doesn’t come close to establishing something that looks like a hierarchy of rights,” said Rob Berschinski, a deputy assistant secretary of state for the Bureau of Democracy, Human Rights and Labor in the Obama administration. “But if it does, repressive governments are going to point to that fact and use it against this, and future administrations, to basically say ‘we are no different than you. You have your priorities, we have ours, now butt out.’”

Committee members were handpicked by Mr. Pompeo’s staff, and most of them are conservatives with strong academic credentials.

In the months after its creation, Mr. Pompeo expressed confidence the panel would create a document that enshrines religious freedom as a central tenant of American human rights policy, which diplomats could refer to for “decades to come.”

The panel is grounded in the vision of Robert George, a Princeton professor and leading proponent of “natural law” theory, a term human rights scholars say is code for “God-given rights” and is commonly deployed in fights to roll back rights for women and L.G.B.T.Q. persons.

“The commission’s charge is not to ‘discover’ new principles,” Mr. George wrote in a document outlining the commission’s vision, “but rather to point the way towards that more perfect fidelity to our nation’s founding principles of natural law and natural rights.”

Early language defining the commission in federal documents echoed Mr. George’s notion, saying the panel would provide “fresh thinking” on human rights discussions, since conversations have “departed from our nation’s founding principles of natural law and natural rights.”

This drew significant criticism from human rights advocates, and since then, the mission has altered to say members will “furnish advice to the secretary for the promotion of individual liberty, human equality, and democracy through U.S. foreign policy.”

The commission is led by Ms. Glendon, a Harvard professor and former ambassador to the Vatican, who has garnered controversy in the past when saying that The Boston Globe receiving the Pulitzer Prize for its investigation into child abuse by priests “would be like giving the Nobel Peace Prize to Osama bin Laden.”

This “is a group of individuals who want to redefine how this country balances human rights interests and to tip the scales in favor of religious freedom, ” said Mark Bromley, chair of the Council for Global Equality, a coalition of 30 human rights groups advocating lesbian, gay, bisexual and transgender rights in American foreign policy.

Two Democratic representatives, Jamie Raskin of Maryland and Joaquin Castro of Texas, warned the commission’s report could “undermine our nation’s ability to lead on critical issues of universal human rights, including reproductive freedom and protections for millions of people globally in the L.G.B.T.Q. community.”

Several human rights organizations have sued the State Department, saying it is violating a federal law that requires advisory panels like the Commission on Unalienable Rights to be “fairly balanced” and transparent with meeting documents at the time of hearings.

The lawsuit is pending, and lawyers representing the State Department said last week the committee would invite public comment on the report before the commission’s work concluded.

Human rights observers warned that any public comment might not change what they predicted to be a preordained outcome to prioritize religious freedom as America’s most valued human right based on Mr. Pompeo’s beliefs and personal interest in the panel.

“Through sheer force of political will and personality,” Mr. Bromley said, “he’s been pushing it forward and has a very clear idea, if you look at his writings and speakings, of where he wants it to end up.”