In recent times, the field of wireless sensor networks (WSNs) has attained a growing popularity in observing the environment due to its dynamic factors. Sensor data are gathered and forwarded to the base station (BS) through a wireless transmission medium. The data from the BS is further distributed to end-users using the Internet for their post analysis and operations. However, all sensors except the BS have limited constraints in terms of memory, energy and computational resources that degrade the network performance concerning the network lifetime and trustworthy routing. Therefore, improving energy efficiency with reliable and secure transmissions is a valuable debate among researchers for critical applications based on low-powered sensor nodes. In addition, security plays a significant cause to achieve responsible communications among sensors due to their unfixed and variable infrastructures. Keeping in view the above-mentioned issues, this paper presents an energy-aware graph clustering and intelligent routing (EGCIR) using a supervised system for WSNs to balance the energy consumption and load distribution. Moreover, a secure and efficient key distribution in a hierarchy-based mechanism is adopted by the proposed solution to improve the network efficacy in terms of routes and links integrity. The experimental results demonstrated that the EGCIR protocol enhances the network throughput by an average of 14%, packet drop ratio by an average of 50%, energy consumption by an average of 13%, data latency by an average of 30.2% and data breaches by an average of 37.5% than other state-of-the-art protocols.