"I wouldn't necessarily look at this as some sort of pattern, but rather two separate incidents," State Department spokesman Mark Toner told reporters at a news conference.
Khan was detained at a New York airport for over two hours by immigration officials after arriving from India in a private plane with Nita Ambani, to address students at Yale University here.
This is second such incident happening with the popular Bollywood Super Star in the US. Khan was also detained in 2009 at the Newark Airport in New Jersey.
The State Department spokesman recommended people to take the benefit of a program in the US Embassy in Delhi under which they can inform the US officials about their stature and their travel plans to the US.
"There is a programme whereby travelers can alert, identify their status before they depart via the embassy. And that's one approach or avenue to take," he said. Toner also ruled out it being a case of racial profiling.
"I think we all know that that's clearly not the case. You know, the fact of the matter is tens of thousands of Muslims travel to and from the US every day and are not detained or delayed," Toner said.
Khan, he said, was temporarily delayed before admission at the White Plains, New York, airport.
"He was traveling to an event at Yale University. We have obviously the utmost respect for Mr Khan and his work, both as an artist and a humanitarian, and we offer our apologies for any discomfort or inconvenience he may have suffered as a result of this incident," Toner said.
India's Deputy Ambassador to the US Arun K Singh conveyed India's sentiment on the issue to Assistant Secretary of State for South and Central Asia Robert Blake. This was followed by a note verbatim on the issue.
"I offered my sincere apologies that he may experienced. I'm not sure that it was done on a personal level," Toner said in response to a question.