Samsung had planned to introduce the app, Samsung Mini Pay, from January and getting it into the app store was the first step in the process.
Samsung had completed testing of the app with some South Korean credit card companies but when it applied for registering the app it received a notice of rejection, the newspaper reported.
No reason was given for the rejection, but the newspaper speculated that it was possible that the app had not met Apple's policies on security and regulations.
The paper quoted a Samsung Electronics representative as saying, "After Apple rejected registration of Samsung Pay Mini onto its app store, we have decided to focus on Smartphones with Android OS."
Apple is apparently thinking of launching its own Apple Pay app in South Korea in the first half of 2017, the paper said, adding that the company's representatives had not provided any indication if this was so when asked.
Samsung Pay, which was launched in August, has so far been used in nine countries. Samsung Pay Mini has been in development for more than a year.