President Donald Trump on Thursday signed his second executive order intended to “protect religious liberty.”

The order establishes a new office at the White House, called the Faith and Opportunity Initiative, that is intended to empower faith-based organizations and “promote religious freedom.” Some civil rights advocates, however, fear it will result in discrimination against lesbian, gay, bisexual and transgender Americans.

“The faith initiative will help design new policies that recognize the vital role of faith in our families, our communities and our great country,” Trump said Thursday, the National Day of Prayer, in the White House Rose Garden. “This office will also help ensure that faith-based organizations have equal access to government funding and the equal right to exercise their deeply held beliefs.”

"Faith is more powerful than government, and nothing is more powerful than God,” Trump, who signed a similar executive order at last year’s National Day of Prayer celebration, continued.

In addition to executive orders, Trump's administration has taken a number of other steps to promote religious liberty, such as January's creation of a new Conscience and Religious Freedom Division inside the Department of Health and Human Services, and October's issuance of new guidance from the Department of Justice prioritizing religious liberty in its litigation strategy.

“This administration has continually promoted the troubling notion that religious freedom is a blank check to discriminate and harm others,” Daniel Mach, director of the ACLU Program on Freedom of Religion and Belief, told NBC News. “This new initiative creates a bureaucratic regime and adopts policy preferences that will worsen that disturbing trend.”

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Both Mach and Camilla B. Taylor, director of constitutional litigation at Lambda Legal, an LGBTQ advocacy group, citied concerns about the new order’s revocation of protections granted in prior executive orders that required service providers receiving government funds to refer beneficiaries to alternative service providers if the initial provider refused to perform certain services for religious reasons.

Taylor noted even if a faith-based service provider is open to referring someone to an alternative provider, it can be difficult if the initial provider is the only one in the area. This was the case for a lesbian couple in Texas, who were denied the opportunity to foster a refugee child because they did not “mirror the holy family.” Taylor said “there is no other agency in that state that performs those services for refugee children.” Lambda Legal is currently suing the Health Department on behalf of the couple.

Taylor called Thursday’s executive order “worrying” and described it as “just the latest assault in a long-term battle that this administration is waging on the members of the LGBTQ community and women in need of reproductive health.”

She said the order constitutes an “invitation” for faith-based groups to apply for public funding, when they have no intention of serving all members of the public. It’s an “unmistakable signal to religious organizations who take government money that they can discriminate without any repercussions whatsoever. It’s open season,” she added.

The Faith and Opportunity Initiative will be headed by an adviser who will help provide a “voice in the White House” for faith-based organizations by making recommendations to the administration, according to a statement issued by the White House. The adviser, who has yet to be named, will alert Attorney General Jeff Sessions to “concerns” by faith-based groups regarding any instances of non-compliance with Sessions’ October 2017 memorandum or the president’s May 2017 executive order.

The adviser will also, according to the new order, “identify and propose means to reduce … burdens on the exercise of religious convictions and legislative, regulatory, and other barriers to the full and active engagement of faith-based and community organizations in Government-funded or Government-conducted activities and programs."

Thursday's executive order comes just weeks before the highly anticipated Supreme Court ruling is expected in the Masterpiece Cakeshop v. Colorado Civil Rights Commission case, which considers whether private businesses have a right to decline service to LGBTQ customers on religious grounds. The White House statement that accompanied the new executive order explicitly mentions the Trump administration’s support of Jack Phillips, the Christian baker at the center of the case, defending his “right to operate his bakery in accordance with his religious beliefs.”

The Alliance Defending Freedom, the conservative Christian legal organization defending Phillips in court, issued a statement Thursday saying Trump’s new executive order “provides hope” that he will “move fully toward fulfilling his promise to protect religious freedom,” but lamenting the president did not go far enough.

“Though we appreciate the spirit of today’s gesture, vague instructions to federal agencies simply leaves them wiggle room to ignore that gesture, regardless of the spirit in which it was intended,” Alliance Defending Freedom President and CEO Michael Farris stated. “We strongly encourage the president to see his campaign promise through to completion and to ensure that all Americans — no matter where they live or what their occupation is — enjoy the freedom to peacefully live and work consistent with their convictions without fear of government punishment.”

Mach of the ACLU said while “religious liberty is a vital, fundamental right,” it is “not a license to discriminate,” which he fears will be the result of the administration’s numerous actions intended to “protect religious liberty.”

“We'll keep an eye on this new initiative to help ensure that government employees and contractors, health care providers, and businesses don't invoke religious freedom to harm LGBTQ people, religious minorities and other vulnerable communities,” he said.

The White House did not respond to NBC News’ request for comment.

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