The bench headed by Chief Justice T S Thakur and A M Khanwilkar, however, granted liberty to the petitioner to approach appropriate authority in the government with his grievances.
It said the petitioner could also approach Telecom Disputes Settlement and Appellate Tribunal (TDSAT) with his plea.
During the hearing the bench did not go into the submissions that the message service applications like WhatsApp's end-to-end encryption feature poses a security risk to the country.
Other than WhatsApp, the petitioner had also named over dozen other messaging platforms like Hike, Viber, Signal, Telegram and Secure chat.
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In his petition, Yadav said that terrorists and criminals could easily communicate on WhatsApp and make plans which are impossible to access even by supercomputers as decrypting a single 256-bit encrypted message would take hundreds of years.