The flight was scheduled to depart at 7:30 a.m. but only took off at around 1 p.m. Tuesday, frustrating travelers who said the delay lasted longer than the journey itself, Times of India newspaper reported.
Video clips Wednesday showed visibly agitated passengers confronting cabin crew as the wait dragged on.
Passengers also said they were not allowed to disembark and had to remain seated inside the aircraft throughout the disruption.
In a statement quoted by the Press Trust of India, the airline said the aircraft returned to the bay due to a minor technical issue.
"While necessary checks and maintenance were being carried out, the cockpit crew exceeded their flight duty time limitations, necessitating a crew change and causing further delay," Indian news site NDTV quoted the airline as saying.
The airline said refreshments were provided and updates shared during the wait while apologizing for the inconvenience.
The incident follows another disruption in January involving an IndiGo flight from Mumbai to Thailand's Krabi, when chaotic scenes unfolded after a pilot declined to operate the flight beyond permitted duty hours.