This “policy of detention and apology by the US cannot continue”, External Affairs Minister SM Krishna said.
Shah Rukh Khan arrived on a private plane and was on the way to Yale University for a function when he was stopped.
US customs and border protection authorities later expressed “profound” apologies for the incident.
The spokesman for the US embassy in Delhi, Peter Vrooman, also apologized “if Mr. Shah Rukh Khan experienced an inconvenience or delay”.
It is not clear why Shah Rukh Khan was detained at the airport, which serves New York City.
In 2009 the actor was detained for two hours at Newark airport and was released after India’s embassy in the US intervened.
Shah Rukh Khan said then that he was stopped because he had a Muslim name. US customs officials denied that the actor had been detained, saying he was questioned.
“Apologies from America have become mechanical,” SM Krishna said on Friday.
He also asked India’s ambassador in the US, Nirupama Rao, to lodge a protest with Washington.
Member of Parliament Rajeev Shukla said the detention was “totally uncalled for”.
The Bollywood film industry has also come out in support of the actor.
“All that the US immigration authorities need to know about Shah Rukh Khan, they can find it at the touch of a button,” musician Javed Akhtar said.
Earlier, the Press Trust of India news agency reported that Shah Rukh Khan was stopped and questioned for more than two hours before being cleared by immigration officials on Thursday.
He was freed after Yale University officials contacted homeland security and customs officials.
“Khan was very, very upset over the episode,” the CNN-IBN channel said, quoting unnamed sources.
Later, Shah Rukh Khan told the students of Yale University that he had been stopped and questioned at the airport.
But, he made light of the incident and joked about it.
“Whenever I start feeling arrogant about myself, I always take a trip to America. The immigration guys kick the star out of stardom,” Shah Rukh Khan said to laughter from the audience.
“They [immigration officials] always ask me how tall I am and I always lie and say 5ft 10 inches. Next time I am going to get more adventurous. [If they ask me] what colour are you, I am going to say white,” he said.
Shah Rukh Khan has appeared in more than 70 films and is considered one of India’s most recognizable and popular celebrities.
There have been several incidents in the past of prominent Indian officials being stopped or frisked at US airports.
In December 2010, the US expressed regret after India’s then-ambassador Meera Shankar was pulled out of an airport security line and frisked by a security agent.
Some reports said she was singled out as she was wearing a sari.
Secretary of State Hillary Clinton said she was concerned about the incident and vowed to prevent a recurrence.
And in 2009, America’s Continental Airlines apologized to former Indian President APJ Abdul Kalam for frisking him before he boarded a flight to the US.
Members of India’s parliament were outraged after it emerged that APJ Abdul Kalam had been frisked and made to remove his shoes at Delhi airport in April.
Protocol exempts former presidents and other dignitaries from such searches.
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