Apple said the problem, an error in the program that installs the new version of iTunes, affected a "limited number" of Mac owners who were running the Mac OS X operating system and had multiple hard drives or hard drive partition.
Apple said it has fixed the problem with a new version and is warning customers to remove the installer.
"While this error is highly unlikely to affect most users, Apple strongly advises that anyone who has downloaded the 2.0 version of iTunes for Mac OS X, as well as anyone who has a beta version of iTunes 2.0 for Mac OS X, immediately remove the iTunes.pkg installer file from their system," the company said on its Web site.
The version with the installer error was only publicly available from Apple from Friday evening to Saturday morning, Apple said on its Web site. An Apple representative was not immediately available for further comment.
Several people on Apple's discussion boards reported the problem.
"I just installed the OS X version of iTunes 2 and it seems to have almost wiped all my non-OS X hard drive partitions clean," wrote one Mac user. "I have a 40GB Maxtor partitioned into 8 sections and a 20GB Maxtor drive. The OS X partition seems to be OK, but, other than a few token folders and files, all my other partitions have been erased."
For those who have lost data, Apple said customers should not perform any operations that would write data on the affected partition and recommended third-party data recovery programs such as Norton Utilities for the Macintosh and TechTool Pro by MicroMat Computer Systems. Those with problems are also encouraged to call Apple's customer service line.
The new version of iTunes was announced last month as Apple introduced the iPod portable music player. In addition to supporting the new device, iTunes 2 adds the ability to burn CDs with music stored in the MP3 format as well as an equalizer and a feature that allows each song being played to fade into the next.