The EU charged Facebook on Tuesday with providing "misleading" information when it sought approval for its blockbuster $22-billion buyout of the WhatsApp mobile messaging service.
The commission said the EU's greenlight of the buyout, announced in October 2014, was not put back into question but the social network could face hundreds of millions of euros in fines.
"The European Commission has sent a Statement of Objections to Facebook alleging the company provided incorrect or misleading information during the Commission's 2014 investigation" of the buyout, the EU's executive arm said in a statement.
With the charge, Facebook joins Google, Amazon and Microsoft among the US-based tech giants caught in major EU competition probes.
Facebook is accused of misleading the EU in a claim that it was technically impossible for it to merge users between the two services.
But in August, WhatsApp said that it would begin sharing data with Facebook, in a bid to allow better-targeted advertising and to fight spam on the platform.
Earlier this year, the EU's powerful competition chief Margarethe Vestager said she "will keep a close eye on how companies use data".
That veiled warning to tech firms came weeks after Vestager ordered Apple to pay back 13 billion euros in taxes and with her team running several cases against Google.
"We respect the Commission's process and are confident that a full review of the facts will confirm Facebook has acted in good faith," a Facebook spokesperson said in an email.