Following the incident, which took place at Chennai airport last week, the Airports Authority of India raised the issue with IndiGo, asking it not to pass the blame for flight delays "falsely" to the ATC, sources said.
One of the sources said the incident prompted IndiGo to send an e-mail to its pilots, instructing them to desist from such acts.
The departure of IndiGo flight 6E-859, operating on the Chennai-Madurai route, had already been rescheduled to 1225 hours from 1145 hours, which was conveyed to passengers via text messages.
The Pilot-in-Command later announced that the flight had been further delayed "because the Air Traffic Controller was not clearing the aircraft for departure", the source told PTI here.
However, the commander was "unaware" of the presence of an ATC among the passengers on the plane.
"After the pilot attributed the delay to the air traffic management team, the controller called up the Chennai
"The ATC then met the pilot through the flight attendant in the cockpit and found that the co-pilot was not in his seat. The pilot was pulled up by the ATC for making a false announcement, blaming the air traffic management team and maligning the reputation of the fraternity in front of the public," the source said.
Later, the commander apologised "unconditionally" for the delay and announced that it was due to the absence of his co-pilot.
IndiGo, in a detailed response, said the flight was delayed by three minutes.
"Our captain while monitoring ground frequency noticed there was ramp and air congestion prevailing on other aircraft and proactively made an announcement citing the same.
"The ATC personnel travelling as a passenger came up and spoke to the captain and our captain made a second announcement," he said.
"Having said that we would have appreciated had the said passenger taken up the issue through proper channel instead of intervening with the operating crew before a flight when they need to focus on procedures and safety," he added.