The tech giant has explained that having a cover over the device could lead to screen damage, stop the ambient light sensor, brightens and True Tone from working properly.
They instead advise users to check if the green light is on to check if the camera is in use.
Apple stated: "If you close your Mac notebook with a camera cover installed, you might damage your display because the clearance between the display and keyboard is designed to very tight tolerances.
Covering the built-in camera might also interfere with the ambient light sensor and prevent features like automatic brightness and True Tone from working. As an alternative to a camera cover, use the camera indicator light to determine if your camera is active, and decide which apps can use your camera in System Preferences."
Apple put out the warning after users reported the issue.
Meanwhile, it has been reported that MacBook Pro laptops with 13.3, 14 and 16-inch screens, and the MacBook Air, will be the first to be powered by a ARM-based silicon chip, that's according to top Apple analyst Ming-Chi Kuo.