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Apple has admitted that the Error 53 message, the users of iPhone 6 see, when they update to iOS 9 or later, is as a result of a Touch ID security protocol laid down by the company.

The error shows up in case of any device that has already been tampered with. In this case, it means that if your device has at some point been repaired by a non-official Apple technician, you will likely come across this error when you upgrade to the latest OS.
Apple devices must be fixed by Apple-certified technicians
The Touch ID is the main victim here. If this fingerprint scanner has at some point fixed by an unofficial technician, you will receive this Error 53 message. According to the company, all fingerprint data is protected using a Secure Enclave which is then paired to the Touch ID in a manner that is unique to it. If this sensor is repaired by a certified Apple technician, the pairing will usually be re-validated. However, in case of a third-party technician, this isn’t hence leading to Error 53.
While you might think staying off iOS 9 or later might be the real deal as far as avoiding Error 53 is concerned, a company spokeswoman said that this message can also be triggered with a factory restore. With this problem, you won’t be able to use your iPhone and in fact, the end result might be buying a new iPhone. This is true, because the unofficial repair done on the phone’s Touch ID means that the warranty has been tampered with.
What really happens here is that the iOS 9 update will check whether your Touch ID sensor matches with other components of the iPhone or iPad as it was made by the company. If there is a mismatch, you will get this Error 53 message, thus rendering your iPhone or iPad unusable.
Lack of sufficient Apple Stores
One thing that might lead to easy violation of the iPhone warranty terms is the lack of Apple Stores in many countries across the globe. What this means is that in case of a damaged iPhone, many have a hard time finding an official Apple technician to take care of the problem. As a result, they end up with unofficial technicians who instead violate the company’s warranty in order to keep the device working properly.
So, whose fault is this? Is it the company’s or the iPhone users’? As it seems (with respect to Error 53), it is the fault of the iPhone user.
The fact that Apple must be the one revalidating the Touch ID shows the high level of security it has put in place with respect to user’s fingerprint data. Some malicious persons might steal personal data during hardware modifications, but with Apple’s iPhone 6, this is not possible.