The Trump administration is “undoing decades of civil and human rights progress” — especially when it comes to LGBTQ issues — according to a new report by the U.S. Commission on Civil Rights, an independent, bipartisan advisory agency.

In its 621-page report, “Are Civil Rights a Reality?,” the commission found that, despite the “extraordinary volume” of civil rights complaints filed in the first two years of the Trump administration, agencies charged with protecting civil rights “generally lack adequate resources to investigate and resolve discrimination allegations within their jurisdiction, leaving allegations of civil rights violations unredressed.”

With respect to lesbian, gay, bisexual, transgender and queer civil rights, the report criticized several policy changes under the Trump administration that have limited the ability of federal agencies to enforce LGBTQ civil rights or redirected efforts toward other priorities.

“In addition to using the budget and other processes to undermine civil rights enforcement, the Administration has also changed course in many substantive civil rights policy areas,” Karen Narasaki, one of the commission’s eight members, stated in the report, which was released last Thursday. “An obvious example is this Administration’s rollback of efforts to combat LGBTQ discrimination.”

“The changes I’ve watched unfold since 2016 are truly unprecedented in the nearly 30 years I have worked in the nation’s Capital,” Narasaki added. “This Administration is not just shifting enforcement priorities, they are undoing decades of civil and human rights progress.”

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Catherine E. Lhamon, the chair of the commission, called the report “overdue” and said the findings about the lack of LGBTQ civil rights enforcement are “devastating.”

“The Trump administration has been as vocal as it is possible to be about its dismissal of LGBTQ rights as worth protecting,” Lhamon told NBC News. “It will take us a very long time to dig out from under the damage this administration has caused to civil rights in this county.”

In a statement, the White House pushed back on the report’s findings and decried efforts by the “radical left” to paint LGBTQ Americans as “threatened.”

“As the first U.S. President in our history to favor same-sex marriage when he was sworn in, President Trump has never considered LGBT Americans second-class citizens and has opposed discrimination of any kind against them,” Judd Deere, special assistant to the president and deputy press secretary, said in an email. “While the radical left has pushed disgusting and false accusations that LGBT Americans are threatened, the President has hired and promoted LGBT Americans to the highest levels of government, including positions at the White House, cabinet agencies, and ambassadorships.”

Deere also noted that earlier this year the Trump administration launched a global campaign to decriminalize homosexuality and put forth a plan to end the HIV epidemic in the U.S. by 2030.

The report is the result of a two-year probe approved in 2017 following “grave concerns” by the commission that budget and personnel cuts by the administration would impede agencies’ ability to protect civil rights. The report, the first of its kind since 2002, draws on publicly available data, information solicited from 13 federal civil rights agencies and bipartisan testimony.

‘Religious freedom over the rights of others’

The report examines several instances across multiple departments where concerns for religious liberty appear to outweigh concerns for LGBTQ rights.

In October 2017, for example, the Department of Justice issuedguidance directing all executive departments and agencies to prioritize “the foundational principle” of religious liberty. In its report, the commission noted that it “received testimony that this new guidance prioritizes religious freedom over the rights of others and may be retrogressive to protecting the rights of LGBT persons.”

A DOJ spokesperson told NBC News the department “disagrees with the report’s findings and stands by its enforcement of civil rights for all citizens.”

The DOJ’s 2017 guidance, according to the report, has had ripple effects across other federal agencies, including the Department of Health and Human Services and the Department of Labor.

The creation of the new Conscience and Religious Freedom Divisionwithin the HHS Office of Civil Rights in January 2018 is one example. The Office of Civil Rights changed its mission statement in May from explicitly ensuring equal access to HHS services to now emphasizing the protection of religious liberty.

“If you look at the ways the agencies talk about what their opportunities are, they changed in dramatic ways,” Lhamon said. She also called the allocation of funding at HHS under the Trump administration “pretty jaw-dropping.”

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The commission report documents how the HHS Office of Civil Rights requested an overall funding decrease from Congress of about $6 million, while allocating new funding to the religious freedom division. According to the report, between fiscal years 2016 and 2017, funding to the direct investigations portion of the HHS Office of Civil Rights decreased by nearly $1.5 million.

When asked about the Commission on Civil Rights’ findings, Roger Severino, director of the HHS Office of Civil Rights, affirmed the office’s commitment to enforcing federal discrimination laws.

“Everyone deserves to be treated with dignity and respect, and we at HHS work to further the health and well-being of all Americans,” he said in a statement.

The Department of Labor’s Office of Federal Contract Compliance Programs, one of the largest civil rights agencies, has also proposed a similar policy change to strengthen religious exemptions available to federal contractors.

In August, the office put forward a rule that would permit federal contractors to “cite religious objections as a valid reason to discriminate against employees on the basis of LGBT status, sex, race, ethnicity, national origin, and other characteristics,” the report states. The rule, which has not yet gone into effect, “would allow federal contractors to fire or refuse to hire an individual because of the person’s sexual orientation, gender identity, status as a pregnant woman or parent, or race, so long as the contractor obtained a religious exemption,” according to the report.

In response to this Labor Department proposal, Commissioner Michael Yaki stated in the report that the “rights of LGBT people to be protected from animus-based discrimination in the workplace are not secure except where states and localities have chosen to provide legal protections and in limited jurisdictions by judicial decision.” He added that the proposed rule demonstrates “no apparent rationale tied to business necessity other than providing a justification for discrimination.”

When asked about the commission’s findings, a DOL spokesperson told NBC News that the Office of Federal Contract Compliance Programs “is fully committed to the enforcement of the prohibitions on discrimination in accordance with the law.”

The definition of ‘sex’

The administration has adopted several policy positions based on a definition of “sex” that defines it as an unchangeable condition determined solely by a person’s biology.

The Department of Justice has taken the position that sex discrimination does not include discrimination on the basis of gender identity, reversing an Obama-era policy that clarified the applicability of Title VII of the Civil Rights Act to include transgender workers.

In February 2017, the departments of Education and Justicerescinded an Obama-era guidance aimed at protecting transgender students from discrimination under Title IX, and in early 2018 confirmed it would not follow up on civil rights complaints by trans students prohibited from using the bathroom corresponding to their gender identity.

The Commission’s report cites evidence collected by the Center for American Progress that found the Trump administration dismissed or administratively closed significantly more discrimination cases related to sexual orientation or gender identity (91.5 percent) than the Obama administration (65.4 percent).

The Department of Education did not respond to a request for comment.

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At HHS, policy changes have reflected the Trump administration’s position on sex and the belief that “providers should not have to refrain from discrimination on the basis of gender identity when providing health care.”

In May, Severino’s office proposed a rule to alter the Affordable Care Act to redefine sex in strictly biological terms, reversing the department’s policy of protecting against gender identity discrimination under Title IX’s prohibition of discrimination on the basis of sex, the report states. The report cites concerns voiced during the public comment period that the proposed rule would create additional obstacles for patients seeking transition-related care.

The commission sent a letter to HHS Secretary Alex Azar “urging HHS not to narrowly define gender to a biological, immutable condition determined at birth.” The report also notes that advocacy groups critical of this proposed rule have said it is “tantamount to pretending that transgender people simply do not exist.”

The report also documents a “notable policy shift” at the Department of Housing and Urban Development regarding the rights of transgender individuals at federally funded shelters. A 2016 Obama-era rule stated that transgender individuals be provided shelter corresponding to their gender identity. However, in May, HUD Secretary Ben Carson proposed a rule that would require homeless shelters to sort people based on biological sex. Carson also allegedly made derogatory comments about transgender women to HUD staffers.

HUD did not respond to NBC News’ request for comment.

Report’s recommendations

In addition to recommending an overall increase in resources allocated to civil rights offices across the board, the report also stressed the importance of collecting information on civil rights abuses disaggregated by sexual orientation and gender identity — a recommendation that goes against the administration’s “concerted effort to roll back data collection from LGBT communities.”

“Federal agencies across the Trump Administration have deleted proposed or existing survey questions relating to LGBT population numbers, older adults, foster youth and parents, crime victimization, and disease prevention,” the report states.

A ‘primal scream’ against President Trump?

Created by Congress in 1957, the Commission on Civil Rights has eight commissioners — four appointed by the president and four by Congress — who serve staggered terms. The commission currently includes four Democrats, three independents and one Republican, and Thursday’s report contains several statements by individual commissioners.

Commissioner Michael Yaki, a Democrat appointed by then-Speaker Dennis Hastert, R-Ill., focused his entire statement on LGBTQ civil rights concerns under the current administration.

“Seemingly no other President has so blatantly and deliberately targeted the rights of the LGBT community,” Yaki said. “Today, after successfully fighting for marriage equality and the repeal of prior discriminatory practices such as ‘don’t ask, don’t tell,’ among other basic freedoms, the LGBT community finds itself once again in a familiar place — being pushed towards the outside looking in, having to summit again the rocky pathway to freedom and equality that was surmounted just scant years ago, all because of a President and an Administration that has chosen intolerance, rather than inclusion, as its first principle.”

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Peter N. Kirsanow, appointed by President George W. Bush and the commission’s sole Republican, fervently disagreed with the assessment offered by the report and his fellow commissioners, calling the report “the progressive civil rights establishment’s primal scream about President Trump.”

“Whether it is HHS protecting conscience and religious liberty rights, the Department of Education attempting to reduce due process abuses in Title IX cases, or DHS attempting to secure the border — Trump Bad,” Kirsanow wrote. “There is no suggestion that people can have good faith policy disagreements, that economic costs are a valid consideration, or that hotly contested cultural issues are in fact hotly contested.”

Lhamon, who was an assistant secretary for civil rights at the Education Department under Obama, pushed back on Kirsanow’s assessment, describing the report as “fair, dispassionate and quite restrained.”

“Had I wanted to primal scream against Trump, there are other things I could have said,” she told NBC News.

Lhamon also noted that a draft of the report was sent to all the agencies reviewed in it for feedback prior to publication and that feedback was incorporated into the report.

“The reality is that there is much to be concerned about,” she said. “Even before the Trump administration, we didn’t fund or staff our civil rights agencies appropriately. It is our job at the commission to call it out.”

Lhamon said she hopes that the report helps “to course correct and ensure that the now six-decade-old promises from Congress are actually lived in the lives of Americans.”