As the two giants fight it out in the smartphone and tablet computer market, the Commission said that in this instance, Samsung appeared to be at fault as the injunctions would prevent Apple from access to core shared patents.
"When companies have contributed their patents to an industry standard and have made a commitment to license the patents in return for fair remuneration, then the use of injunctions against willing licensees can be anti-competitive," EU Competition Commissioner Joaquin Almunia said in a statement.
The Commission said it had informed Samsung that its injunctions over Apple access to Standard-Essential Patents (SEPS) "amounts to an abuse of a dominant market position prohibited by EU anti-trust rules."
While Samsung "will continue to fully cooperate with the commission", the company said it "is confident that in due course the commission will conclude that we have acted in compliance with European Union competition laws."
Brussels opened a probe in January after Samsung sought injunctions banning the sale of products made by its competitors in several European countries, alleging that they were illegally using its patents.