One of the highlights of the iPhone 5S, the fingerprint scanner, is facing two concerns that may take a little shine off Apple's cool new feature. Privacy advocates have raised concerns over how Apple plans to handle this highly sensitive data.

And many consumers who ran out to pick up the new iPhone when it went on sale Friday may find themselves at odds with their information technology departments. Few companies and government agencies allow their employees to use fingerprint IDs to unlock iPhones being used for work. It may take months or longer before these businesses adopt the new technology.

The iPhone 5S is the first Apple device with a built-in fingerprint scanner on the home button. Instead of entering a four-digit code, a user needs only to place their finger on the button to unlock their phones. Apple says it will only store the data on the device in an encrypted format rather than sending it to its own servers. Apple will also block third-party apps from accessing what the company calls "iTouch ID."