In June, Judge Richard Posner in Chicago threw out cases that Motorola, now owned by Google, and Apple had filed against each other claiming patent infringement. Both companies appealed.

In rejecting the Google case, Posner barred the company from seeking to stop iPhone sales because the patent in question was a standard essential patent.

This means that Motorola Mobility had pledged to license it on fair and reasonable terms to other companies in exchange for having the technology adopted as a wireless industry standard.

Standard essential patents, or SEPs, are treated differently because they are critical to ensuring that devices made by different companies work together.

Google appealed to the U.S. Court of Appeals for the Federal Circuit. The FTC said in its court filing that Posner had ruled correctly.

The commission, which has previously argued against courts banning products because they infringe essential patents, reiterated that position on Wednesday.

"Patent hold-up risks harming competition, innovation, and consumers because it allows a patentee to be rewarded not based on the competitive value of its technology, but based on the infringer's costs to switch to a non-infringing alternative when an injunction is issued," the commission wrote in its brief.

The case is Apple Inc. and NeXT Software Inc. V. Motorola Inc. and Motorola Mobility Inc., in the U.S. Court of Appeals for the Federal Circuit, no. 2012-1548, 2012-1549.

(Reporting By Diane Bartz)

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