Khan was reportedly released after the Indian consul intervened on his behalf.
News of Khan's detention sparked outrage in India, with the government in New Delhi complaining that there had been too many similar incidents for Indians travelling in the US.
"I am of the opinion that the way we are frisked - for example I too was frisked - we should also do the same to them," Ambika Soni, the information and broadcasting minister, said.
"I don't understand how in the name of religion, frisking can be done for anyone like this."
Last week, there was uproar after Abdul Kalam, a former Indian president, was frisked by personnel of US carrier Continental Airlines in New Delhi before being allowed to board a US-bound flight.
Protocol rules at Indian airports exempt certain dignitaries from security checks and the airline later apologised to Kalam.
Timothy Roemer, the US ambassador in the Indian capital, sought to play down Saturday's incident, describing Khan as a "global icon" who was always welcome in the US.
"We are trying to ascertain the facts of the case to understand what took place," he said.
But Mahesh Bhatt, a leading Indian film producer, said the questioning of Khan was an example of the mood of "Islamophobia" in the US.
"I am not surprised because the attitude towards Muslims in the United States post the 9/11 [attacks] and after [former US President George] Bush - the Islamophobia wave - has been particularly harsh," he said.