The European Commission said Facebook had said it could not automatically match user accounts on its own platform and WhatsApp.
But two years later it launched a service that did just that.
Facebook said the errors it had made were not intentional.
In a statement, the Commission said: "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."
However, it added that the fine would not reverse its decision to clear the $19bn purchase of WhatsApp and was unrelated to separate investigations into data protection issues.
EU Competition Commissioner Margrethe Vestager said: "Today's decision sends a clear signal to companies that they must comply with all aspects of EU merger rules, including the obligation to provide correct information.
"And it imposes a proportionate and deterrent fine on Facebook. The Commission must be able to take decisions about mergers' effects on competition in full knowledge of accurate facts."
In statement, Facebook said: "We've acted in good faith since our very first interactions with the Commission and we've sought to provide accurate information at every turn.
"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."