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The solar flares and geomagnetic storms are considered a potential threat for the upcoming Indian Regional Navigation Satellite System or Navigation with Indian Constellation (NavIC). Therefore, we investigated in detail the occurrence of tracking failure and effects on the positional accuracy of the NavIC L5-band and S-band system under direct exposure of X2.2 and X9.3 solar flare on September 6, 2017, X9.3 is the strongest event since the NavIC signals are in the service. The regional NavIC data (5–6 September 2017) from the equatorial region Trivandrum station and the Equatorial Ionization Anomaly area in India (Surat, Bombay, Hyderabad and Gandhinagar stations), are collected using the accord NavIC dual-frequency (L5-band and S-band) receivers. We have shown that the 1G NavIC signals remain in loss of lock condition for 1 h on September 6, 2017 (X2.2 and X9.3 solar flares), and as a result, positioning accuracy deviated on September 6, 2017. Hence, the solar flare event considered a potential threat for future NavIC based autonomous navigation technologies. [ABSTRACT FROM AUTHOR]