Industry players have committed to license innovations essential to industry standards on fair, reasonable and non-discriminatory (FRAND) terms. This means the patent owner cannot dictate who is allowed to use its patent and the licensing fee cannot be excessive.
The European Commission (EC) said in a statement that it will examine whether Motorola's behaviour amounts to an abuse of a dominant market position.
Motorola has pledged to work closely with the EC to resolve the matter. "Motorola Mobility is confident that a thorough investigation will demonstrate that it has honoured its FRAND obligations and complied with anti-trust laws," the company said in a statement.
Apple previously clashed with Motorola over the amount it should pay for its use of a patent, which led a German court to order a ban of certain iPad and iPhone models in Germany last year. However, Apple later won a suspension of Motorola's ban on iPad and iPhone sales.
Apple was also forced to suspend its push e-mail service to German customers as a result of another dispute.
Microsoft faces a complaint in Germany later this month over its use of H.264 video-compression technology patents claimed by Motorola.
Microsoft plans to move its European software distribution centre from Germany to the Netherlands to prevent a potential ban of shipments of its Windows 7 system software and Xbox 360 consoles.
Patent consultant Florian Mueller said in a blog that the EC's intervention might influence the outcome of the case. Judges in Germany have shown a "worrying tendency" to put patent law above anti-trust law, he wrote.
The EC raised concerns about Motorola's enforcement tactics when granting approval for Google's acquisition of the firm.
At the time, EU competition commissioner Joaquin Almunia said the EC would keep a close eye on the behaviour of all market players, particularly the increasingly strategic use of patents.