The hands-on search last week also embarrassed the university officials who invited Meera Shankar, India's ambassador to the United States, to give a speech for an international studies program.
"It was a wonderful program, maybe the best we've had, (but) this stupid incident ruined the whole thing. She said, 'I will never come back here,"' said Janos Radvanyi, chair of Mississippi State University's international studies department. "We are sending her a letter of apology."
But a Transportation Security Administration spokesman said diplomats are not exempt from the searches and that Shankar "was screened in accordance with TSA's security policies and procedures."
What happened to Shankar reflects the strong emotions surrounding the TSA's pat-down procedures, and raises questions about the proper handling of diplomats as well as foreign travelers with different styles of dress.
Officials at the Indian embassy in Washington declined to discuss what happened.
Radvanyi, the Mississippi State educator, said Shankar, 60, spoke at a university program last Friday.
A Jackson police officer escorted Shankar to Jackson-Evers International Airport on Saturday for a flight to Baltimore, Radvanyi said, and she was taken to a VIP waiting room.
The officer informed airport police that Shankar was an ambassador, but she was later pulled from a security line and patted down by a female TSA agent, Randvanyi said.
The Clarion-Ledger newspaper of Jackson quoted witnesses as saying Shankar was told she was singled out for additional screening because of her dress. She had on a sari, which drapes across the body and is worn by many Indians.
The TSA has come under fire for new security measures including body scanners and pat-downs that critics say intrude on the privacy of airline passengers.
The TSA spokesman, Nicholas Kimball, said there are a number of factors that could prompt a pat-down, including bulky clothing, but he said the agency doesn't generally discuss specific cases. Passengers at some airports are asked to undergo a body scan, but the Jackson airport doesn't have them yet.
Shankar is a career diplomat who has served as Indian ambassador since April 2009. Among her earlier postings was as ambassador to Germany.
India's relations with the United States have been cool at times - partly because of U.S. ties to India's traditional rival, Pakistan. However, relations between the U.S. and India have grown closer in recent years.
Radvanyi said it took weeks to arrange for Shankar to speak at the program, but he's concerned she won't return and that her treatment at the airport might discourage other international guests from coming.
Shankar also met with Mississippi state officials during her trip.
Radvanyi said at least one official from the Mississippi Development Authority, the state's economic agency, witnessed the search, which was reportedly conducted in a booth or room with transparent walls.
Kimball said anyone who asks for a private screening will be taken to a room out of view from the public. It's not clear if Shankar asked for the search to be done in private.
"Mississippi has always had a good relationship with the Indian government and we hope that this unfortunate incident does not damage the perceptions Indian officials have of Mississippi," MDA spokeswoman Melissa Medley said in a statement.
A spokesman for Gov. Haley Barbour said federal authorities are aware of the situation and it's up to them to handle it.
Kimball said less than 3 percent of passengers receive a pat-down.