Apple's deal with Samsung faces investigation by South Korea's Fair Trade Commission (FTC).
The organisation confirmed it is "currently reviewing the facts" of the case.
"We are investigating whether Samsung has been unfairly supplying flash memory chips to Apple at cheaper prices than applied to domestic music player makers," a spokesman told Reuters.
The investigation follows last month's report that a possible joint investment between Apple and Samsung had collapsed, due to local opposition and a potential FTC investigation.
Apple had been considering entering into a joint $3.8 billion investment in a new plant with the South Korean firm. This week the company confirmed a $1.25 billion investment across multiple companies: Hynix, Intel, Micron, Samsung Electronics and Toshiba.
Samsung began supplying flash memory chips to Apple this year.