The present disclosure relates to a method and system for detecting root cause for software failure and hardware failure. The system comprises a debugging unit with one or more preconfigured communication protocols. The debugging unit identifies one or more debugging issues and performs protocol level transactions with the hardware, participating in the system integration, through a suitable communication protocol. The debugging unit also determines status of the protocol level data transaction based on whether a data read failure has occurred during this transaction. The status is unsuccessful when there is a data read failure in the data transaction and the status is successful otherwise. The root cause for the failure is detected to be one of the hardware components when the status is unsuccessful and the software application when the status is successful. Finally, the detected root causes are resolved using appropriate techniques.