The Commission says Facebook misled it when the company said it was impossible to match users’ Facebook and WhatsApp accounts.
But in August, WhatsApp said it would do just that, by linking users’ phone numbers with their Facebook identities.
Facebook said it had nothing to hide and had acted in good faith.
The Commission believes the ability to link the accounts of the two services’ users must have existed in 2014, though this is vigorously disputed by Facebook.
If the Commission concludes that it was definitely misled, either by accident or design, it could fine Facebook up to 1% of its turnover, which would amount to hundreds of millions of euros.
“Companies are obliged to give the Commission accurate information during merger investigations,” said Commissioner Margrethe Vestager, who is in charge of competition policy,
“In this specific case, the Commission’s preliminary view is that Facebook gave us incorrect or misleading information during the investigation into its acquisition of WhatsApp.”
Facebook is being asked to respond by 31 January 2017.
For its part, it says that it was only very early this year that it found a way to establish a link with the accounts of WhatsApp users, via their phone numbers.
And even so, Facebook says in fact it still cannot match accounts with the precision needed for full “cross-platform messaging”, which it argues was the Commission’s main concern back in 2014.
“We’re pleased that the Commission stands by its clearance decision, and we will continue to cooperate and share information officials need to resolve their questions,” he added.
The Commission said its new probe would not undermine its previous decision to approve the $19bn (£16bn) merger of the two companies because it had not relied on the misleading information alone to approve the deal.