The two technology companies are embroiled in more than 20 legal disputes in 10 countries.
"The (European) Commission has indeed sent requests for information to Apple and Samsung concerning the enforcement of 'standards-essential' patents in the mobile telephony sector," the European Commission said in a statement on Friday.
"Such requests for information are standard procedure in antitrust investigations, to allow the Commission to establish the relevant facts in a case. We have no other comments at this stage," it added.
Standards-essential patents means they have been incorporated in internationally accepted technology standards, which in the case of Samsung and Apple, means 3G and UMTS technology.
Samsung said in a statement it had "at all times remained committed to fair, reasonable and non-discriminatory (FRAND) licensing terms" for its wireless standards-related patents.
"We have received a request for information from the European Commission and are cooperating fully," it said.
Apple declined to comment.
In an October 28 filing with a California court, the U.S.-based firm said Samsung's lawsuits related to its patents was "so egregious that the European Commission recently has opened an investigation to determine whether Samsung's behavior violates EU competition laws."
The Commission investigation is more likely to target Samsung rather than Apple, said intellectual property expert Florian Mueller.
"Only Samsung enforces allegedly standards-essential patents, and the capacity in which Apple received the Commission's requests for information must therefore be that of a witness and maybe also that of an informal or formal complainant," he said.
Samsung has brought patent infringement claims against Apple in several EU courts, accusing its rival of not paying licensing fees for some of its patents before Apple started selling iPhones.
A Dutch court dismissed Samsung's arguments last month, saying its 3G patents were part of essential standards which should be open to license under FRAND terms.
Such patent tactics should worry regulators, Mueller said.
"Samsung went too far by trying to shut down Apple's products with its 3G patents in nine different countries on four continents. That's a recipe for triggering antitrust intervention," he said.
"This investigation has huge implications for Apple's dispute with Samsung, but way beyond those two companies, it's about the kind of licensing commitment the entire technology industry relies upon."
The Commission can fine a company up to 10 percent of its global turnover if it is found to have violated EU rules.
(Additional reporting by Hyunjoo Jin in Seoul; Editing by David Holmes and Jon Loades-Carter)