"The Commission has sent out questionnaires as part of a preliminary investigation into Google’s and Facebook’s data practices," a Commission spokeswoman told AFP.
"These investigations concern the way data is gathered, processed, used and monetised including for advertising purposes," she added.
The Commission did not say who exactly the questionnaires were sent to. It is a step that could lead to a formal investigation.
Facebook vice president Nick Clegg was asked about the probe during a press conference in Brussels but did not answer directly.
Facebook faces investigations worldwide, he said.
Clegg nonetheless warned EU regulators not to let themselves get misled by faulty reasoning when it comes to data.
"This phrase you often hear that data is oil is deeply unhelpful because data is nothing like oil," Clegg said.
"It's not something that you suck out of the ground and burn in a vehicle engine and that's it. Data is infinitely divisible and infinitely sharable," he added.
"Data is something that you can both share and keep at the same time," Clegg noted.
"For a data intensive companies like FB we would urge regulators and legislators not to be trapped by analog parallels which don’t apply to the digital world," he said.
A Google spokesman said in an e-mail to AFP: "We use data to make our services more useful and to show relevant advertising, and we give people the controls to manage, delete or transfer their data.
"We will continue to engage with the Commission and others on this important discussion for our industry."
In September 2016, European Competition Commissioner Margrethe Vestager warned that she would keep a close eye on companies that collect and use data such as Facebook, WhatsApp or Google.
Since she began working at the commission in November 2014, Vestager has hit Google with three major fines for abusing its dominant market position in different sectors.
Vestager has been promoted to vice president in the new European Commission and still holds the competition portfolio in addition to a new one on regulation of the digital sector.
Meanwhile on Monday, Facebook announced a new tool for Irish users to easily transfer photos and video footage towards Google Photos, which is owned by its competitor.
Facebook said it would extend the service at some point to other countries and internet platforms.