On Friday, the Centers for Disease Control and Prevention purged from its website thousands of pages that included terms such as “transgender,” “L.G.B.T.” and “pregnant person,” to comply with an executive order barring any material that promoted “gender ideology.”

By Monday, some of the pages had reappeared, in part in response to intense media coverage, backlash from the scientific community and concern for the public’s health, according to a senior official with knowledge of the matter.

The purge had also swept up vaccine information statements, which must be given to patients before they can be immunized; guidelines for contraception; and several pages on how race and racism affect health outcomes. Also removed was a database containing 20 years of H.I.V. data that doctors rely on to determine whether a pregnant woman lives in an area of high H.I.V. prevalence and should be tested for the virus in her third trimester.

Some of these resources were also reinstated, but the return was not entirely smooth. Charts and tables in the H.I.V. database could be reached through a Google search, for instance, but the C.D.C.’s own portal remained broken.

C.D.C. employees are “fully and completely implementing the executive order,” said a senior official who spoke on condition of anonymity for fear of retaliation. But “historical data, articles, and clinical guidelines continue to be available,” the official said. “That essentially is how this is being applied.”

The shake-up accompanied two other directives also aimed at expunging information on certain topics. C.D.C. scientists were ordered late on Friday to withdraw any pending publications, at any scientific journal, that mention the forbidden terms, according to an email viewed by The New York Times.

Separately, a directive prohibiting C.D.C. employees from holding scientific meetings or communicating with other organizations or the public was indefinitely extended on Saturday, when it was expected to lapse, according to another email obtained by The Times.

“I am very fearful and I am very angry about what is happening right now,” said Dr. Ina Park, an expert in H.I.V. and other sexually transmitted infections at the University of California, San Francisco.

The directive also targeted pages on other government websites, including a webpage on Section 1557 of the Affordable Care Act, under the aegis of the Health and Human Services Department. That provision forbids “discrimination on the basis of race, color, national origin, age, disability, or sex (including pregnancy, sexual orientation, gender identity, and sex characteristics), in covered health programs or activities.” It, too, was back online on Monday.

The C.D.C.’s recommendations are the bedrock of clinical practice in the United States. Every hospital’s procedural manuals are filled with the agency’s documents, and clinicians regularly refer to the recommendations, on the website or through the agency’s app.

Now, however, searching for some terms leads to a dead link or to pages that have been stripped of key details, or the search yields a suggestion to explore another topic instead. For instance, a search for the word “abortion” suggests that the user “also try: adoption.”

Some pages — for instance, those on transgender health — were expected to remain absent because they might promote “gender ideology.”

“I have no idea what that term means,” said Dr. Richard Besser, who served as acting director of the C.D.C. in 2009.

“We’re not talking here about ideology — we’re talking about public health,” he added. “We’re talking about people whose lives are being put at risk.”

The disappearance of the pages is already affecting medical care. In Washington State, Dr. Tim Menza, a medical director for King County’s sexual health clinic, worried that hard-won progress against early syphilis in gay and bisexual men would be lost.

Dr. Jessica Weyer, an obstetrician-gynecologist in Concord, N.H., said she could not guide her patients’ choice of contraception without access to the complex eligibility criteria. For instance, the guidelines for birth control include recommendations for patients with various medical conditions. They also list drug interactions that must be taken into account and give providers information on newer methods like vaginal rings.

“If a patient has high blood pressure or migraine headaches, I need to know what’s safe for her,” Dr. Alison Stuebe, an obstetrician-gynecologist in North Carolina, said.

The C.D.C. website is ostensibly being altered to comply with Mr. Trump’s executive orders on diversity, equity, inclusion, accessibility and “defending women.” But vaccine information statements and contraception guidelines are unrelated to those orders, Dr. Weyer said.

“This just seems like a purposeful removal of important information providing safe contraception, which I view as terrifying,” she said. “It sounds like they want to control women, not defend women.”

Although the executive orders did not mention race, several resources on structural racism and health disparities in certain communities also disappeared on Friday.

In the United States, race and ethnicity are strongly linked to health. Black and Native American women are two to three times as likely as white women to die during pregnancy and after childbirth, and their babies face roughly twice the risk of dying before their first birthday. Diabetes, obesity and other chronic diseases are also much more prevalent, and life expectancy is lower, among racial and ethnic minority groups.

Information on racial disparities is crucial for helping health care providers to focus on the groups most at risk, said Linda Goler Blount, president of the Women’s Black Health Imperative, an advocacy group. During the Covid pandemic, she noted, health researchers discovered that pulse oximeter devices, which measure blood oxygen levels, “didn’t work on people with dark skin.” That disparity might have contributed to higher death rates among communities of color.

“If we can’t collect data by race, ethnic identity and gender identity, we’re going to see mortality rates increase,” Ms. Blount said.

Mr. Trump’s orders purged more than 8,000 web pages across more than a dozen U.S. government websites. In some cases, the executive orders also targeted the work of private citizens.

A memo to the federal Agency for Healthcare Research and Quality, which publishes papers from both government and academic researchers, gave employees until 5 p.m. on Friday to scrub the agency’s publication, Patient Safety Network, of terms including “transgender,” “nonbinary,” “L.G.B.T.” and “gender identity.”

Among the roughly 20 research papers that were taken down was one from 2022 detailing how clinicians can better identify emergency room patients at risk of suicide. The paper’s lead author, Dr. Gordon Schiff, is the director of quality and safety for the Harvard Medical School Center for Primary Care; he is not a government scientist. The paper was flagged for a single line: “High risk groups include male sex, being young, veterans, Indigenous tribes, lesbian, gay, bisexual, transgender, queer/questioning (L.G.B.T.Q.).”

Dr. Schiff said he was shocked by the new administration’s “extreme censorship.” “This whole idea that the risk factors or commentary should be based on political ideology rather than data and truth is a pretty scary prospect,” he said.

Some experts are exploring the legality of the administration’s deleting content from federal websites and papers written by C.D.C. scientists. But in the case of Dr. Schiff’s paper, the administration clearly crossed the line, said Larry Gostin, director of the World Health Organization Center on Global Health Law.

“To me, that’s classic viewpoint censorship in violation of the First Amendment,” Mr. Gostin said.

“While the administration may be able to silence government health officials carrying out their official duties, it cannot drag private scientists into its web of censorship,” he added. “And all that censorship for expressing a single word with which the government objects.”