The investigation is focusing on whether Samsung has been supplying Flash memory chips to Apple at cheaper prices than it applies to domestic music player makers.
The Fair Trade Commission claims that the investigation began a while ago and covered Samsung's earlier deals with Apple.
Small South Korean manufacturers of digital music players have complained that Samsung is offering the chips used in Apple's iPod players at an unfairly low price, thus putting them at a disadvantage.
Analysts believe that the investigation is unlikely to have serious repercussions for Samsung. Apple declined to comment.
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