Designing a reliable system on reconfigurable devices has become a significant factor for implementing mission critical applications like communication protocols, automotive, nuclear reactor control, and remote applications. With the improvement in fabrication technology, logic density of the field programmable gate arrays has increased rapidly. Because of decrease in feature size, integrated circuits are becoming vulnerable to errors and also the ageing component results in run time faults. FPGAs when used in harsh conditions like high radiation and temperatures, there is a possibility of getting affected by transient faults or the soft errors. In digital communication, safety and confidentiality of data is achieved through a suitable encryption algorithm. Encryption is most important aspect when it comes to security. Reliable design techniques are very much necessary for maintaining the system's normal function. Many of the available techniques are based on redundancy logic causing area overhead for the design. Through this paper, an implementation is illustrated for managing soft errors or the single event upsets. Proposed methodology identifies and avoids the errors occurring at the logic resources where the encryption algorithms are mapped on the device. Thus encryption algorithms work normally without getting affected by the errors. During the simulation process, errors are injected at the configuration memory frames and monitored using a Single event-upset manager (SEM) controller. The proposed design is implemented on Zedboard using Xilinx Vivado 2017.4.