His aides and ministers are said to be sharing information on the messaging app ahead of June's historic in/out referendum.
Unlike emails sent on Downing Street computers, WhatsApp messages, which are encrypted, cannot be released under Freedom of Information laws.
And furious Eurosceptics last night accused Mr Cameron’s team of "trying to hide their secrets" from voters.
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Matthew Elliott, the CEO of anti-EU group Vote Leave, slammed the move.
He said: "Cameron's taxpayer-funded spin doctors are trying to hide their secrets from the public.
"This is potentially criminal and should be investigated by the Cabinet Office’s Head of Ethics and the Information Commissioner."
And Tory MP David Davis urged the Government to "learn from the mistakes" of US politician Hillary Clinton, who was caught sending emails on a private account.
He added: "Attempts to avoid the Freedom of Information Act will lead to scandal and embarrassment.
"This will only reinforcing the public's view that the Remain campaign is prepared to cheat to win this referendum."
Ministers Sajid Javid, Stephen Crabb and Nicky Morgan are known to be WhatsApp users, but all denied discussing the referendum on the app.
But a spokesman for George Osborne refused to confirm or deny whether the Chancellor uses the service.
A Downing Street source told the Sun: "This is the modern age, people communicate in variety of different ways."