The European Commission said the US social network inaccurately claimed it would be unable to combine user data between the two companies' accounts.
"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 Facebook staff were aware of such a possibility," the commission said.
It added that the ruling does not affect its decision to approve the merger.
Commissioner Margrethe Vestager, who has recently put the tax affairs of a number of high-profile firms including Apple, Amazon and Google under the microscope, said the sanction was "proportionate and deterrent".
She added: "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."