According to the flight's captain, he was not consulted before the airline took the decision.
"While Mr. Kamra's behaviour was unacceptable and verbally abusive, at no point did he not comply with crew instructions," the Captain said in his letter to IndiGo's management.
"Mr. Kamra's behaviour, while unsavoury, was not qualifying of a level 1 unruly passenger. Indeed, we pilots can all attest to incidents similar or worse in nature that were not deemed unruly," he said.
The letter further read: "I was disheartened to learn that my airline has taken action in this case solely on the basis of social media posts, with no consultation whatsoever with the Pilot-in-Command."
IndiGo in a statement said: "We have received the relevant statements and the internal committee has initiated the investigation regarding this incident."
Meanwhile, Civil Aviation Minister Hardeep Singh Puri on Thursday tweeted: "I had expressed my views with regard to the unruly behaviour of a passenger onboard @IndiGo6E flight.
"I reiterate that airlines must ensure 'Zero Tolerance' for any activity which has the potential to jeopardise safety of Passengers in an Aircraft."
Passenger carriers IndiGo, Air India, SpiceJet and GoAir have barred the stand-up comedian for allegedly portraying "unacceptable behaviour".
On Tuesday, IndiGo had barred the stand-up comedian for six months from using its services for allegedly portraying "unacceptable behaviour" onboard one of its flights.
It has been alleged that Kamra, while travelling on a Mumbai-Lucknow IndiGo flight, provoked a TV news anchor by asking questions over his news presentation style.
On his part, Kamra had posted a statement on his Twitter handle on Tuesday which read: "Today I met Arnab Goswami in a flight to Lucknow, and politely asked him to have a conversation. At first, he pretended to be on a phone call. I waited for his so-called phone call to get over. Seatbelt signs were off at this time. I gave him a monologue about what I felt about his 'Journalism'. He refused to answer any questions, he called me 'mentally unstable'."
In another tweet, Kamra said: "Thank you Indigo a six month suspension is honestly very kind of you... Modiji might be suspending Air India forever."
( With inputs from IANS )