Taking a strong note of the incident, a video clip of which went viral on Tuesday, Raju asserted that fisticuffs have no place in a civilised society.
He said aviation regulator DGCA would be asked to submit an independent report and the Bureau of Civil Aviation Security (BCAS) would check whether certain procedures were violated as the incident took place in the security area.
In a seven-page letter submitted to the ministry, IndiGo said action was taken against staff for the "regrettable incident".
Fisticuffs of any kind have to be condemned and "we want to condemn these kinds of incidents", Raju told reporters here.
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The Directorate General of Civil Aviation (DGCA) has been asked to submit an independent report on the incident, he said while stressing that such barbarous things should not happen.
Minister of State for Civil Aviation Jayant Sinha termed the incident as "shocking and deplorable" and said safety and security of passengers cannot be compromised.
"At the very outset, let me start off by acknowledging that we were at fault and we not only apologise for this regrettable incident, we have also taken action," IndiGo President and Whole Time Director Aditya Ghosh said in the letter.
Stressing that any violation on the airside is dangerous, Raju said, "I understand that some of them (procedure) have not been followed and notice will go from the BCAS as to why things have not been followed".
"We can't have violations. These are incorrect. Can there be fisticuffs on the airside, what is this?," he remarked.
About the incident, Choubey said "this is not on" and that the BCAS has been asked to suspend the airport entry permits of the three IndiGo staff.
Providing a chronology of events along with some screen shots, Ghosh said in the letter that he had apologised to the passenger on the same day the incident took place and the employees involved were immediately suspended.
"...we recognised that whatever may have been the provocation, my colleagues should have exercised restraint," Ghosh said.
While Katyal might have felt that Thomas was rude, the letter said, the reality is that the latter was "only trying to ensure to the safety of Katyal and prevent an accident" as he was moving towards catering high lift.
"The irony of the fact is that Juby Thomas was indeed doing his work and ensuring safety of passengers," the letter noted.
However, when the passenger could not hear Thomas, the latter "started shouting in a much louder voice to overcome the very loud ambient noise around the aircraft", which might have been construed as rude by Katyal, it said.
Out of three employees involved, IndiGo said it terminated the services of Montu Kalra while warning letters were issued to Thomas and Sahiv Sharma.
IndiGo said that Kalra, who is claiming to be the whistle blower, is the one who is shouting in the video and instructing the two other junior colleagues to prevent Katyal from boarding the bus.
The airline said Kalra "instigated the incident".
"It is important for us to point out that Montu Kalra was not terminated because he either shot a video or as he is now claiming, brought this (incident) to our attention," the report said.
In the video, Katyal is first seen being stopped from entering a coach, and then being pulled back by a ground staff. Another airline employee is seen restraining Katyal.
The passenger is seen fighting back and falling to the ground in the melee.
The shares of IndiGo's parent InterGlobe Aviation fell over 2 per cent to close at Rs 1,181.75 on BSE.
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