The social network was accused by the commission of falsely claiming that it was impossible to automatically merge user information from WhatsApp and Facebook. This followed a decision taken by WhatsApp last summer to share data with Facebook for advertising purposes, a practice which was halted in November.
The European Commission said in a statement: "The Commission has found that, contrary to Facebook's statements in the 2014 merger review process, the technical possibility of automatically matching Facebook and WhatsApp users' identities already existed in 2014, and that Facebook staff were aware of such a possibility."
Facebook has hit back by saying it "acted in good faith" since its very first interactions with the Commission. "We’ve sought to provide accurate information at every turn," the company added. "The errors we made in our 2014 filings were not intentional and the Commission has confirmed that they did not impact the outcome of the merger review. Today’s announcement brings this matter to a close."
The news also comes follows on from an ultimatum handed to Facebook, Google and Twitter over illegal terms of service in March by EU consumer protection agencies.