The flag was found in several photographs of the person accused of the South Carolina church massacre.
Apple has voluntarily taken down several civil war games from its App Store, as they featured the controversial Confederate flags.
The Confederate battle flag was one of three designs that served as the official national flag of the Confederate States of America.
However, it has became controversial after the recent South Carolina church massacre, where the accused 21 year old Dylann Roof was spotted carrying the flag in several of his social media photos.
South Carolina Governor Nikki Haley also asked lawmakers to take down the Confederate battle flag at the state capitol grounds.
Reuters cited game developing company Hunted Cow spokesperson as saying "They (games) will be resubmitted with an earlier confederate flag."
The company also confirmed that ‘Civil War 1862’, ‘Civil War 1863’, ‘Civil War 1864’ and ‘Civil War Gettysburg’ have been removed from the app store because its content featured the now controversial flag.
Apple is not the only tech giant to remove content featuring the Confederate flag as eBay, Amazon and Google pulled out Confederate flag merchandise from their sites.
Wall Mart and Sears have also become the part of the movement as they have stopped selling the flag.