Motorola won an injunction in Germany over Apple products that used patents relating to data transmission technology in February 2012.
The EU Competition Commission claim that Motorola sought an injunction despite Apple's apparent willingness to enter talks and reach an agreement with the US owned company.
Apple offered to pay Motorola a licence fee for using the patents - but the two companies could not agree on a price.
Apple products, including the iPhone, were taken off sale during the dispute.
Several models of the smartphone, and the iPad, were removed from sale on Apple's German website - but were still available in other stores in the country.
In a statement, the commission said: "while recourse to injunctions is a possible remedy for patent infringements, such conduct may be abusive where standard-essential patents are concerned and the potential licensee is willing to enter into a licence on fair, reasonable and non-discriminatory terms."
EU Competition Commissioner Joaquin Almunia added: "The protection of intellectual property is a cornerstone of innovation and growth. But so is competition.
"I think that companies should spend their time innovating and competing on the merits of the products they offer - not misusing their intellectual property rights to hold up competitors to the detriment of innovation and consumer choice."
The BBC said that the dispute revolves around the use of what are known as standard-essential patents (SEPs) - patents that are deemed essential to the operation of standards such as mobile phone signal.
In this case Motorola's innovation is deemed crucial to the GPRS data transmission standard used by GSM cellular networks across the world.
Holders of SEPs are obliged to licence the patent's use to competitors in return for a fee on so-called fair, reasonable and non-discriminatory (Frand) terms. In simpler terms - a fair price.
The commission's stance forms part of its "preliminary view" on the case. Motorola is able to defend its position ahead of the final decision.
Motorola spokeswoman Katie Dove told AFP: "We agree with the European Commission that injunctions should only be sought against unwilling licensees and, in this case, Motorola Mobility followed the procedure established.
"Apple had to make six offers before the court recognised them as a willing licensee."