Mark Zuckerberg has publicly said Facebook Inc. allows its more than three billion users to speak on equal footing with the elites of politics, culture and journalism, and that its standards of behavior apply to everyone, no matter their status or fame.

In private, the company has built a system that has exempted high-profile users from some or all of its rules, according to company documents reviewed by The Wall Street Journal.

The program, known as “cross check” or “XCheck,” was initially intended as a quality-control measure for actions taken against high-profile accounts, including celebrities, politicians and journalists. Today, it shields millions of VIP users from the company’s normal enforcement process, the documents show. Some users are “whitelisted”—rendered immune from enforcement actions—while others are allowed to post rule-violating material pending Facebook employee reviews that often never come.

At times, the documents show, XCheck has protected public figures whose posts contain harassment or incitement to violence, violations that would typically lead to sanctions for regular users. In 2019, it allowed international soccer star Neymar to show nude photos of a woman, who had accused him of rape, to tens of millions of his fans before the content was removed by Facebook. Whitelisted accounts shared inflammatory claims that Facebook’s fact checkers deemed false, including that vaccines are deadly, that Hillary Clinton had covered up “pedophile rings,” and that then-President Donald Trump had called all refugees seeking asylum “animals,” according to the documents.

A 2019 internal review of Facebook’s whitelisting practices, marked attorney-client privileged, found favoritism to those users to be both widespread and “not publicly defensible.”

“We are not actually doing what we say we do publicly,” said the confidential review. It called the company’s actions “a breach of trust” and added: “Unlike the rest of our community, these people can violate our standards without any consequences.”

Despite attempts to rein it in, XCheck grew to include at least 5.8 million users in 2020, documents show. In its struggle to accurately moderate a torrent of content and avoid negative attention, Facebook created invisible elite tiers within the social network.

In describing the system, Facebook has misled the public and its own Oversight Board, a body that Facebook created to ensure the accountability of the company’s enforcement systems.

In June, Facebook told the Oversight Board in writing that its system for high-profile users was used in “a small number of decisions.”

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The documents that describe XCheck are part of an extensive array of internal Facebook communications reviewed by The Wall Street Journal. They show that Facebook knows, in acute detail, that its platforms are riddled with flaws that cause harm, often in ways only the company fully understands.

Moreover, the documents show, Facebook often lacks the will or the ability to address them.

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Time and again, the documents show, in the U.S. and overseas, Facebook’s own researchers have identified the platform’s ill effects, in areas including teen mental health, political discourse and human trafficking. Time and again, despite congressional hearings, its own pledges and numerous media exposés, the company didn’t fix them.

Sometimes the company held back for fear of hurting its business. In other cases, Facebook made changes that backfired. Even Mr. Zuckerberg’s pet initiatives have been thwarted by his own systems and algorithms.

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For ordinary users, Facebook dispenses a kind of rough justice in assessing whether posts meet the company’s rules against bullying, sexual content, hate speech and incitement to violence. Sometimes the company’s automated systems summarily delete or bury content suspected of rule violations without a human review. At other times, material flagged by those systems or by users is assessed by content moderators employed by outside companies.

Mr. Zuckerberg estimated in 2018 that Facebook gets 10% of its content removal decisions wrong, and, depending on the enforcement action taken, users might never be told what rule they violated or be given a chance to appeal.

Users designated for XCheck review, however, are treated more deferentially. Facebook designed the system to minimize what its employees have described in the documents as “PR fires”—negative media attention that comes from botched enforcement actions taken against VIPs.

If Facebook’s systems conclude that one of those accounts might have broken its rules, they don’t remove the content—at least not right away, the documents indicate. They route the complaint into a separate system, staffed by better-trained, full-time employees, for additional layers of review.

Most Facebook employees were able to add users into the XCheck system, the documents say, and a 2019 audit found that at least 45 teams around the company were involved in whitelisting. Users aren’t generally told that they have been tagged for special treatment. An internal guide to XCheck eligibility cites qualifications including being “newsworthy,” “influential or popular” or “PR risky.”

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The lists of those enrolled in XCheck were “scattered throughout the company, without clear governance or ownership,” according to a “Get Well Plan” from last year. “This results in not applying XCheck to those who pose real risks and on the flip-side, applying XCheck to those that do not deserve it (such as abusive accounts, persistent violators). These have created PR fires.”

In practice, Facebook appeared more concerned with avoiding gaffes than mitigating high-profile abuse. One Facebook review in 2019 of major XCheck errors showed that of 18 incidents investigated, 16 involved instances where the company erred in actions taken against prominent users.

Four of the 18 touched on inadvertent enforcement actions against content from Mr. Trump and his son, Donald Trump Jr. Other flubbed enforcement actions were taken against the accounts of Sen. Elizabeth Warren, fashion model Sunnaya Nash, and Mr. Zuckerberg himself, whose live-streamed employee Q&A had been suppressed after an algorithm classified it as containing misinformation.

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Historically, Facebook contacted some VIP users who violated platform policies and provided a “self-remediation window” of 24 hours to delete violating content on their own before Facebook took it down and applied penalties.

Mr. Stone, the company spokesman, said Facebook has phased out that perk, which was still in place during the 2020 elections. He declined to say when it ended.

At times, pulling content from a VIP’s account requires approval from senior executives on the communications and public-policy teams, or even from Mr. Zuckerberg or Chief Operating Officer Sheryl Sandberg, according to people familiar with the matter.

In June 2020, a Trump post came up during a discussion about XCheck’s hidden rules that took place on the company’s internal communications platform, called Facebook Workplace. The previous month, Mr. Trump said in a post: “When the looting starts, the shooting starts.”

A Facebook manager noted that an automated system, designed by the company to detect whether a post violates its rules, had scored Mr. Trump’s post 90 out of 100, indicating a high likelihood it violated the platform’s rules.

For a normal user post, such a score would result in the content being removed as soon as a single person reported it to Facebook. Instead, as Mr. Zuckerberg publicly acknowledged last year, he personally made the call to leave the post up. “Making a manual decision like this seems less defensible than algorithmic scoring and actioning,” the manager wrote.

Mr. Trump’s account was covered by XCheck before his two-year suspension from Facebook in June. So too are those belonging to members of his family, Congress and the European Union Parliament, along with mayors, civic activists and dissidents.

While the program included most government officials, it didn’t include all candidates for public office, at times effectively granting incumbents in elections an advantage over challengers. The discrepancy was most prevalent in state and local races, the documents show, and employees worried Facebook could be subject to accusations of favoritism.

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Facebook recognized years ago that the enforcement exemptions granted by its XCheck system were unacceptable, with protections sometimes granted to what it called abusive accounts and persistent violators of the rules, the documents show. Nevertheless, the program expanded over time, with tens of thousands of accounts added just last year.

In addition, Facebook has asked fact-checking partners to retroactively change their findings on posts from high-profile accounts, waived standard punishments for propagating what it classifies as misinformation and even altered planned changes to its algorithms to avoid political fallout.

“Facebook currently has no firewall to insulate content-related decisions from external pressures,” a September 2020 memo by a Facebook senior research scientist states, describing daily interventions in its rule-making and enforcement process by both Facebook’s public-policy team and senior executives.

A December memo from another Facebook data scientist was blunter: “Facebook routinely makes exceptions for powerful actors.”

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To minimize conflict with average users, the company has long kept its notifications of content removals opaque. Users often describe on Facebook, Instagram or rival platforms what they say are removal errors, often accompanied by a screenshot of the notice they receive.

Facebook pays close attention. One internal presentation about the issue last year was titled “Users Retaliating Against Facebook Actions.”

“Literally all I said was happy birthday,” one user posted in response to a botched takedown, according to the presentation.

“Apparently Facebook doesn’t allow complaining about paint colors now?” another user complained after Facebook flagged as hate speech the declaration that “white paint colors are the worst.”

“Users like to screenshot us at our most ridiculous,” the presentation said, noting they often are outraged even when Facebook correctly applies its rules.

If getting panned by everyday users is unpleasant, inadvertently upsetting prominent ones is potentially embarrassing.

Last year, Facebook’s algorithms misinterpreted a years-old post from Hosam El Sokkari, an independent journalist who once headed the BBC’s Arabic News service, according to a September 2020 “incident review” by the company.

In the post, he condemned Osama bin Laden, but Facebook’s algorithms misinterpreted the post as supporting the terrorist, which would have violated the platform’s rules. Human reviewers erroneously concurred with the automated decision and denied Mr. El Sokkari’s appeal.

As a result, Mr. El Sokkari’s account was blocked from broadcasting a live video shortly before a scheduled public appearance. In response, he denounced Facebook on Twitter and the company’s own platform in posts that received hundreds of thousands of views.

Facebook swiftly reversed itself, but shortly afterward mistakenly took down more of Mr. El Sokkari’s posts criticizing conservative Muslim figures.

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