Over last few years, e governance in India has made rapid progress and adopted global best practices in terms of citizen-centricity, reach, connectivity, efficiency, transparency, accountability and availability. Multiple modes and ease of access, seamless connectivity and availability, user friendliness and efficiency of e Governance services have opened up avenues making e-Governance services most prone to serious security risks. International trends and domestic experiences show that the e-governance services are constant target of organized crime by hackers and prominent government sites are being probed daily. The security threat landscape for e Governance applications constantly changes and new type of vulnerabilities keeps manifesting. In today’s race to build cutting-edge e Governance business solutions, web applications are being developed and deployed with lesser attention to critical and widespread security threats. Government can no longer afford to tolerate security issues with high risk values which could hinder delivery of services and impact the confidentiality, integrity and availability of information. To mitigate with appropriate countermeasures and security controls, it is required to evaluate and estimate risks associated with e-Governance applications security issues that can be exploited. In this context, this paper outlines the risk rating methodology from e Governance perspective to estimate risk associated with security issues at application layer that are critical and widespread.