Some users had complained about the fact that Songs of Innocence had automatically been downloaded to their devices without their permission.
It had not been immediately obvious to many of the account holders how to delete the tracks.
The US tech firm is now providing a one-click removal button.
"Some customers asked for the ability to delete 'Songs of Innocence' from their library, so we set up itunes.com/soi-remove to let them easily do so. Any customer that needs additional help should contact AppleCare," spokesman Adam Howorth told the BBC.Users who want to remove the new U2 album can now click a button to do so
Users who remove the album and do not download it again before 13 October will be charged for the 11 tracks if they subsequently try to add them again.
"It's embarrassing for Apple that it's had a bit of a backlash," commented Ian Maude from the media consultancy Enders Analysis.
"It was giving something away to its customers - so that part was really good - but what it should have probably done was make it optional. Not everybody's a U2 fan as it's just discovered.
"Is there any long-term impact? No. It's moved very quickly to fix the problem."'Blood, sweat and tears'
Apple made the album available to about 500 million iTunes customers in 119 countries to coincide with its iPhone 6 and Watch launch event last week.Some users had requested an easy way to delete the music from their media libraries
U2's singer Bono acknowledged at the time that not everyone would appreciate the gift.
"People who haven't heard our music, or weren't remotely interested, might play us for the first time because we're in their library," he wrote on the band's site.
"And for the people out there who have no interest in checking us out, look at it this way? the blood, sweat and tears of some Irish guys are in your junk mail."
Bono added that Apple had "paid" for the giveaway, and reports have suggested that prime placement of banner ads publicising the album on the iTunes store and other publicity provided by the tech firm might be worth as much as $100m (?62m).
Sales of earlier U2 albums have re-entered iTunes' charts and the band has also raised its profile ahead of an expected tour as well as a planned follow-up album called Songs of Experience.Apple is promoting U2's new music as well as offering earlier albums at discounted prices
The new tracks on Songs of Innocence have, however, split the critics.
The Drowned in Sound site suggested that U2 no longer had it in them to make a great album, adding that giving away songs for free had "somewhat devalued a record that cost six years of their lives and a lot of money to make".
But Rolling Stone magazine gave the album its maximum score, saying that it was "a triumph of dynamic, focussed renaissance".