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The study presents the comprehensive assessment of the Indian Institutions of National Importance (IoNI) website’s privacy and security practices. These 130 IoNI websites were selected because of the status conferred to premier institutions by the Government of India. This empirical study was based on webometric methods that assessed the quantitative aspects of information technologies structures on the web. The study also employed content analysis for analyzing the sites privacy policies. The assessment reveals numerous security vulnerabilities like the adoption of HTTPS may not always provide better protection to their users because 39 websites do not have TLS encrypted connection; still 62 websites use the older encryption TLS 1.2 version. Though Google tracking is moderately prevalent in 53 websites, only 4 websites enabled the privacy protection parameters. Also, only 26 percent of the 130 websites have privacy policies, yet their readability score is very poor. It was also found that none of the websites provides a cookie consent form or opt-in/opt-out option on their landing page. This may indicate that institutions are not concerned with the current privacy and security standard. Finally, based on the analysis, recommendations are made like increasing users' awareness, implementing simple privacy policy, reducing unnecessary tracking through informed consent, and promoting the use of privacy-enhancing technologies. Web tracking is common, yet few studies demonstrate its extent and consequences from academic websites context. It is hoped that these valuable insights into the current state of privacy and security may incite the need for updated information security.