Even though, there are many advantages of biometrics security system, it still has many flaws in its system. Each biometrics application method has weaknesses which can cause problems for its users. For example, if the biometrics security system uses fingerprints to identify its users and an accident causes a user to lose his/her finger then it can be a problem during the verification process. For voice recognition methods, illnesses such as strep throat can make it hard for authorized users to get access to their information. Another factor that can influence voice recognition systems is the continuous aging of its users. Noise in an environment where voice recognition is used to identify its users can also make it hard for users to be identified.

For iris or retinal scanning applications, users may find it very intrusive. Users may also have the concern for the safety of their eyes during the iris or retinal scan. Furthermore, databases used to store user identification data will be very large which might form a potential threat. For scanning retinal/iris characteristics and storing large amount of database, biometrics system requires new and modern technology. Therefore, the cost for equipment is also expensive. Finally, lots of people are still concerned about biometrics technology in different aspects such as: security, adaptability to rate of change in life, scalbility, accuracy, privacy and others.