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The groups, the Electronic Privacy Information Center and the Center for Digital Democracy, say that WhatsApp's privacy policy doesn't match up with Facebook's, and that Facebook has a long history of violating users' privacy.
According to the complaint, WhatsApp has a "strong commitment to user privacy," whereas Facebook's current service collects and stores "virtually all available user data."
The complaint (PDF) reads:
WhatsApp built a user base based on its commitment not to collect user data for advertising revenue. Acting in reliance on WhatsApp representations, Internet users provided detailed personal information to the company including private text to close friends. Facebook routinely makes use of user information for advertising purposes and has made clear that it intends to incorporate the data of WhatsApp users into the user profiling business model. The proposed acquisition will therefore violate WhatsApp users' understanding of their exposure to online advertising and constitutes an unfair and deceptive trade practice, subject to investigation by the Federal Trade Commission.
But, Facebook insists that users actually shouldn't worry too much, because it intends to keep the two entities separate.
A Facebook spokesperson told CNET's Seth Rosenblatt in a statement: "As we have said repeatedly, Whatsapp will operate as a separate company and will honor its commitments to privacy and security."
The FTC has not yet responded to the complaint.