BRUSSELS—The European Union charged Meta Platforms over its systems for handling illegal content on Facebook and Instagram, the first such allegation against a social-media platform under the bloc’s flagship online-content rules.

The European Commission, the EU’s executive arm, said Friday that Meta fails to give users a simple way to flag illegal content such as sexual abuse of children and terrorist material. It also accused the company of not giving its users adequate tools to appeal content-moderation decisions when their posts are removed or their accounts are suspended.

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The charges risk provoking the ire of the Trump administration, which has complained in the past that the EU’s digital regulations unfairly target U.S. companies and that the bloc is trying to censor Americans.

President Trump has threatened tariffs in response to the EU and other jurisdictions’ fines and digital regulations. The EU reached a tariff agreement with the U.S. in the summer that officials hope will limit further duties, but talks are continuing over the deal’s implementation.

The Commission said Friday that its case against Meta over users’ rights to appeal content-moderation decisions shows that the EU law protects free speech. It allows EU citizens “to fight back against unilateral content moderation decisions taken by big tech,” a spokesman said.

Meta said the company disagreed with any suggestion that it breached the EU’s online-content rules and will continue to negotiate with the Commission. Meta has already changed its policies in the EU, a spokesman said, and is “confident that these solutions match what is required under the law.”

The preliminary charges come under EU legislation called the Digital Services Act, which aims to set standards for how tech giants including Apple, Meta and Google-parent Alphabet should police online content. Breaches of the law can lead to fines of up to 6% of a company’s global annual revenue.

The EU’s findings aren’t final, and Meta will have a chance to review the allegations and respond to the Commission.

Meta was also accused on Friday of making it difficult for researchers to access public data. The EU levied the same allegation about researchers’ data access against TikTok.

TikTok said it is committed to transparency and values researchers’ contributions, but that there is a tension between the EU’s requirements for data sharing and its data privacy rules.

The Commission hasn’t yet issued a fine under the Digital Services Act, although it has opened more than a dozen investigations over the past two years related to advertising transparency, illegal products and other potential breaches.

The EU issued preliminary findings last year against Elon Musk’s social-media platform X over grievances related to the company’s advertising rules, researchers’ access to data and the design of the platform’s blue check marks. A separate investigation looking at the spread of illegal content on X and the platform’s measures to deal with information manipulation is ongoing.

Musk and X’s then chief executive, Linda Yaccarino, responded to the preliminary findings at the time, saying they stood with those who believed in the open flow of information and supported innovation.

Write to Kim Mackrael at kim.mackrael@wsj.com

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