The incident comes days after a passenger was assaulted and dragged on the tarmac at the Delhi airport by the staff of IndiGo airlines in a video that was widely shared.
Ms Urvashi Parekh Viren was injured in the accident and was rushed to a hospital where she was being treated.
"Our IndiGo representative was pushing her wheelchair towards the arrival hall. As he was guiding her wheelchair through a vehicular lane, which was dimly lit at that time of the night, her wheelchair got stuck in a deep crack on the tarmac and lost balance and she fell off her wheelchair," the airline said in a statement.
According to the airline, the passenger was kind enough to say that it was not a human error and "we should deal with the staff with empathy, when we de-brief our loader. We promised to do so."
An inquiry into the incident was ordered by Civil Aviation Minister Ashok Gajapati Raju and the airline was asked to explain.
The video, compared to United Airlines dragging a passenger off an overbooked flight in April, has caused waves of shock and anger against India's most successful budget airline.