In a notice on its website, the consumer protection body said that Samsung had organized an Internet campaign in violation of fair trade rules to praise Samsung smartphones while slamming those of HTC.
Earlier this year the FTC fined Samsung NT$300,000 for misleading advertising about the camera functions on its Galaxy Y Duos GT-S6102 phone.
The FTC action comes with HTC badly on the defensive amid disappointing sales for its once popular smartphones.
The company, which posted its first quarterly loss in the July-September period, has suffered a drop in its global handset market share from a high of 10.3 percent in the third quarter of 2011 to only 2.6 percent in the third quarter of 2013.
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