The US network cut the segment which included his dance tribute to victims of the July 7 London bombings during Friday's (July 27) event.
His tribute featured 50 dancers performing to the backing of 'Abide With Me', sung by Emeli Sandé.
NBC did not air the segment during their exclusive US coverage of the opening ceremony, instead opting to show an interview between Ryan Seacrest and swimmer Michael Phelps.
The network insisted that they were not informed that the dance sequence was a tribute to the 2005 attacks.
"I am really sad that I couldn't show the work in America, and that really upsets me, because I don't think it's any less or more than any of the other pieces," Khan told The AP.
"Is it not accessible enough? Is it not commercial enough? It brings to mind the question - but maybe I'm wrong because I don't really know the reason - but it brings to mind a question that maybe it's too truthful, and I think that says it all really."
NBC also did not air the tribute to people inside the stadium's loved ones who had died.
The network aired a time-delayed edited version of the ceremony, in order for it to go out during primetime in the US.
"We are live streaming every sporting event, all 32 sports and all 302 medals… The opening and closing ceremonies, however, are entertainment spectacles," the network said in a statement.
"Our award-winning production team will present them on a medium that best demonstrates their grandeur and majesty, and at a time when friends and family are able to gather together to watch, which is in primetime."
The London 2012 opening ceremony saw record viewing figures for NBC on Friday.
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