"We recently discovered a manufacturing issue affecting a very limited number of iPhone 5s devices that could cause the battery to take longer to charge or result in reduced battery life," an Apple spokeswoman told the New York Times.
Apple customers encountering malfunctioning batteries in an iPhone 5S would be offered new devices, she said.
"We are reaching out to customers with affected phones and will provide them with a replacement phone," the spokeswoman said.
Out of the millions of 5s handsets sold so far several thousand units are thought to be affected by the battery problems, the Times reported.
Apple has reported sales of nine million of its newest 5S and 5C iPhones in the three days following their launch in September, but did not detail how many of each device were bought.
The battery problems have been limited to the 5S version, Apple said.