Samsung is being investigated over whether it breached antitrust rules by accusing rivals of infringing on its patent rights.
South Korea's Samsung, the world's top maker of smartphones, is involved in a patent tussle with Apple in courts across 10 countries including the United States, Australia, France and Japan. Apple is also Samsung's biggest customer.
Samsung sought injunctions last year in various EU countries against competitors, saying they infringed some of its patent rights, which are considered essential to European mobile telephony standards.
Samsung pledged in 1998 to license its patents to the European Telecommunications Standards Institute on fair, reasonable and non-discriminatory (FRAND) terms.
"The (European) Commission will investigate, in particular, whether in doing so (seeking injunctions on patent infringements in 2011) Samsung has failed to honour its irrevocable commitment given in 1998 to the European Telecommunications Standards," the EU executive said.
"In order to guarantee undistorted competition and to reap the positive economic effects of standardisation it is important that FRAND commitments be fully honoured by the concerned undertakings."
The EU Commission said it would investigate whether Samsung was abusing its dominant position through such actions.
Samsung had no immediate comment.
The case underlines the clash between intellectual property rights and competition rights, said Matthew Levitt, a partner in Brussels at law firm Hogan Lovells.
"The Commission is stepping in, saying this is a competition case as it has done in the past, for example in the Microsoft licensing case," he said.
Motorola Mobility, which is being acquired by Google and is also battling Apple over its patents, and other companies tempted to take the legal route should take note, said independent patent expert Florian Mueller.
"Even though Samsung is at this stage the only company to be investigated over this issue, other suspected abusers could face similar inquiries anytime," Mueller said.
"And everyone else who may intend to seek or enforce injunctions based on FRAND-pledged standards-essential patents in Europe will now have to proceed with extra caution."
Motorola has one of the mobile industry's largest patent libraries.
Samsung's main competitors in the mobile device market are Apple, Finland's Nokia and Blackberry maker, Canada's Research in Motion, as well as other makers of phones using Google's Android software.
The European Commission is able to fine companies up to 10 per cent of their global turnover if it finds them in breach of EU competition rules.