The problem affected less than 1 per cent of the video iPods that were available for purchase after September 12.
The company has received less than 25 reports concerning the problem, Apple said on its website.
The iPods got the virus from a Windows computer at one of its manufacturing plants, Apple said.
The virus, RavMonE.exe, is known to spread through external data storage devices when they are connected to computers and affects only machines running the Windows operating system from Apple rival Microsoft Corp.
Security experts say the virus opens up further security holes for hackers.
Up-to-date anti-virus software included with most Windows computers should detect and remove it, Apple said.
Though the iPods themselves are not affected, nor Apple's Mac OS computers, Apple recommended that iPod owners use its latest iTunes program to remove the virus from their new devices.
Other iPod models were not affected and all video iPods now shipping are virus-free, the company said.
"As you might imagine, we are upset at Windows for not being more hardy against such viruses, and even more upset with ourselves for not catching it," the company stated.
Profits up
Apple's profits have jumped 24 per cent from a year ago, with the sales of iPod music players and Macintosh computers soaring.
More than 39 million iPods and 5.3 million Macs have been sold over the past year.
The company recorded a 546 million dollar profit ($A726.6 million) in the last quarter.