Gone is “I Know Why the Caged Bird Sings,” Maya Angelou’s transformative best-selling 1970 memoir chronicling her struggles with racism and trauma.

Two copies of “Mein Kampf” by Adolf Hitler are still on the shelves.

Gone is “Memorializing the Holocaust,” Janet Jacobs’s 2010 examination of how female victims of the Holocaust have been portrayed and remembered.

“The Camp of the Saints” by Jean Raspail is still on the shelves. The 1973 novel, which envisions a takeover of the Western world by immigrants from developing countries, has been embraced by white supremacists and promoted by Stephen Miller, a senior White House adviser.

“The Bell Curve,” which argues that Black men and women are genetically less intelligent than white people, is still there. But a critique of the book was pulled.

The Trump administration’s decision to order the banning of certain books from the U.S. Naval Academy’s library is a case study in ideological censorship, alumni and academics say.

Political appointees in the Department of the Navy’s leadership decided which books to remove. A look at the list showed that antiracists were targeted, laying bare the contradictions in the assault on so-called diversity, equity and inclusion policies.

“Initially, officials searched the Nimitz Library catalog, using keyword searches, to identify books that required further review,” Cmdr. Tim Hawkins, a Navy spokesman, said in a statement on Friday. “Approximately 900 books were identified during the preliminary search. Departmental officials then closely examined the preliminary list to determine which books required removal to comply with directives outlined in executive orders issued by the president.”

“This effort ultimately resulted in nearly 400 books being selected for removal from the Nimitz Library collection,” he added.

At most university libraries, books that the Navy’s civilian leadership banned — like “The Second Coming of the KKK,” Linda Gordon’s account of how the Klan gained political power in the 1920s — and “The Camp of the Saints” would coexist on nearby shelves.

The Naval Academy, a 179-year-old institution in Annapolis, Md., has produced generations of military officers, many of whom have become leaders in industry, Congress and the White House. The Department of the Navy’s purge of 381 books there picked sides in the racism debate, and those that examine and criticize historical and current racism against Black Americans lost.

To academics, there is real concern that the actions of the Navy’s civilian leaders run counter to the purpose of higher education, as well as to the academy’s stated mission to educate midshipmen “morally, mentally and physically” so that they can one day “assume the highest responsibilities of command, citizenship and government.”

“I think it does a real disservice to the students to suggest that they can’t handle difficult ideas or face ideas they disagree with,” said Risa Brooks, a professor of political science at Marquette University. “We are training these people to go out and command troops and to lead people potentially in war. We want them to be resilient, because what they’re going to face is far worse than a book on a bookshelf with a title that possibly makes them uncomfortable.”

“That’s really underestimating them,” she added.

In response to an order by the office of Defense Secretary Pete Hegseth, civilian Navy officials picked the books that were removed from the academy’s Nimitz Library, which contains nearly 600,000 publications, reference texts, novels and works of nonfiction.

Officials began pulling books off the library’s shelves the evening of March 31 and completed the purge the next morning, before the defense secretary visited that day.

The actions have caused a stir among some of the school’s alumni, who include four-star admirals and generals as well as other high-ranking government and elected officials.

“The Pentagon might have an argument — if midshipmen were being forced to read these 400 books,” said Adm. James G. Stavridis, an author, academy alumnus and former commander of all U.S. forces in Europe. “But as I understand it, they were just among the hundreds of thousands of books in the Nimitz Library which a student might opt to check out. What are we afraid of keeping from them in the library?”

One of the admiral’s recent books specifically cited Ms. Angelou’s memoir as a valuable resource for helping military leaders understand the diversity of viewpoints that make up the armed forces.

“Book banning can be a canary in a coal mine and could predict a stifling of free speech and thought,” he added. “Books that challenge us make us stronger. We need officers who are educated, not indoctrinated.”

William Marks, an alumnus of the academy and a retired Navy commander, set up a GoFundMe campaign to purchase books from the banned list and provide them to academy midshipmen.

“These are among the most intelligent students in the world, who we are entrusting to go to war,” he said. “What does this say about the Pentagon if they don’t trust these young men and women to have access to these books in the library?”

Commander Marks is working with a bookstore in Annapolis to have a banned books table where midshipmen can get a free book from the list. He aims to expand the effort to hand out books at off-campus events such as Naval Academy football games.

“Conservatives should be just as outraged at banning books as liberals are,” he said. “This should be a bipartisan issue.”

Representatives Adam Smith of Washington and Chrissy Houlahan of Pennsylvania, both Democrats, denounced the removal of the books in a letter on April 4 to John Phelan, the Navy secretary.

They called the move “a blatant attack on the First Amendment and a clear effort to suppress academic freedom and rigor” at the school and “an alarming return to McCarthy-era censorship.”

The purge at the library is extremely rare and possibly unprecedented at an institute of higher education, said Philomena Polefrone of American Booksellers for Free Expression, a group representing independent booksellers.

“Most of these books are not about D.E.I.,” she said, referring to diversity, equity and inclusion. “They’re by or about L.G.B.T.Q.+ people, or Black people, or anyone who is not a white, cisgender, heterosexual man.”

The Naval Academy is accredited by the Middle States Commission on Higher Education, which last certified the school in June 2016. The commission’s criteria for schools include “a commitment to academic freedom” and a climate that should foster “respect among students, faculty, staff and administration from a range of diverse backgrounds, ideas and perspectives.”

In a statement, Nicole Biever, the commission’s chief of staff, said her organization was aware of reporting about the books being removed from the academy’s library but was not reconsidering the school’s accreditation as a result. The commission sent a letter to colleges and universities on Feb. 14, Ms. Biever noted, that offered help in maintaining their credentials while also “ensuring compliance with all applicable legal or government requirements,” such as executive orders from the White House.

With President Trump’s political ideology beginning to curtail academic freedoms, Professor Brooks said that discussing one of the now-banned books in class could have added value for future military officers.

“Libraries don’t have these books because they are indoctrinating people,” she said. “They can help expose them to different ideas they may not have encountered before.”

It is similar to a point made by Gen. Mark A. Milley, the former chairman of the Joint Chiefs of Staff, during testimony before the House Armed Services Committee, where Republican members complained that the military academies were teaching “critical race theory.”

“I’ve read Mao Zedong. I’ve read Karl Marx. I’ve read Lenin,” General Milley said at the hearing, in June 2021. “That doesn’t make me a communist.”

He then offered an argument for expanding political studies in the service of defending the Constitution after the Jan. 6 attack on the Capitol.

“I want to understand white rage, and I’m white, and I want to understand it,” the general continued. “What is it that caused thousands of people to assault this building, and try to overturn the Constitution of the United States of America?”

That books touching on racism would be banned from a library dedicated in honor of Fleet Adm. Chester W. Nimitz, a 1905 academy graduate and five-star naval hero of World War II, seems incongruous with his actions during the war, when the military was still racially segregated.

Notably, in 1942, Admiral Nimitz personally bestowed the service’s second-highest valor award, the Navy Cross, to a Black enlisted sailor named Doris Miller for his courageous actions during Japan’s attack on Pearl Harbor.

Admiral Nimitz recognized the historical significance of the award at the time.

“This marks the first time in this conflict that such high tribute has been made in the Pacific Fleet to a member of his race,” the admiral said. “And I’m sure that the future will see others similarly honored for brave acts.”