A college student who came to the United States as an Iraqi refugee was removed from a Southwest Airlines flight in California earlier this month after another passenger became alarmed when she heard him speaking Arabic.

The student, Khairuldeen Makhzoomi, a senior at the University of California, Berkeley, was taken off a flight from Los Angeles International Airport to Oakland on April 6 after he called an uncle in Baghdad to tell him about an event he attended that included a speech by United Nations Secretary General Ban Ki-moon.

“I was very excited about the event so I called my uncle to tell him about it,” he said.

He told his uncle about the chicken dinner they were served and the moment when he got to stand up and ask the secretary general a question about the Islamic State, he said. But the conversation seemed troubling to a nearby passenger, who told the crew she overheard him making “potentially threatening comments,” the airline said in a statement.

Mr. Makhzoomi, 26, knew something was wrong as soon as he finished his phone call and saw that a woman sitting in front of him had turned around in her seat to stare at him, he said. She headed for the airplane door soon after he told his uncle that he would call again when he landed, and qualified it with a common phrase in Arabic, “inshallah,” meaning “god willing.”

“That is when I thought, ‘Oh, I hope she is not reporting me,’ because it was so weird,” Mr. Makhzoomi said.

That is exactly what happened. An Arabic-speaking Southwest Airlines employee of Middle Eastern or South Asian descent came to his seat and escorted him off the plane a few minutes after his call ended, he said. The man introduced himself in Arabic and then switched to English to ask, “Why were you speaking Arabic in the plane?”

Mr. Makhzoomi said he was afraid, and that the employee spoke to him “like I was an animal.”

“I said to him, ‘This is what Islamophobia got this country into,’ and that made him so angry. That is when he told me I could not go back on the plane.”

Zahra Billoo, the executive director of the San Francisco Bay Area office of the Council on American-Islamic Relations, said there had been at least six cases of Muslims being pulled off flights so far this year. The conduct of Southwest Airlines was of particular concern, she said, after another Muslim passenger was removed from a flight in Chicago last week.

“We are concerned that Muslims are facing more and more scrutiny and baseless harassment when they are attempting to travel,” Ms. Billoo said.

Brandy King, a spokeswoman for Southwest Airlines, said the company was unable to comment on the conduct of individual employees. Efforts on Saturday to contact the employee in Los Angeles, whose name was provided by Mr. Makhzoomi, were unsuccessful.

“We regret any less than positive experience a customer has onboard our aircraft,” the company said in a statement. “Southwest neither condones nor tolerates discrimination of any kind.”

Law enforcement officials arrived shortly after Mr. Makhzoomi accused the airline employee of anti-Muslim bias, he said. He was brought into the terminal and searched in front of a crowd of onlookers while half a dozen police officers, including one with a dog, stood watch.

Three agents from the Federal Bureau of Investigation arrived and brought him into a private room where they questioned him, he said. They asked about his mother, who lives with him and his younger brother in Oakland. They also asked about his father, Khalid Makhzoomi, a former Iraqi diplomat who was jailed in Abu Ghraib prison by Saddam Hussein and later killed by the dictator’s regime, according to Mr. Makhzoomi. His family came to the United States in 2010.

Mr. Makhzoomi said an F.B.I. agent told him the Southwest Airlines employee who was upset by the allegation of anti-Muslim bias said a passenger reported hearing him talk about martyrdom in Arabic, using a phrase often associated with jihadists. He denied the charge and was allowed to return to the terminal, he said, where the same Arabic-speaking employee refunded his ticket.

A spokeswoman for the F.B.I. in Los Angeles, Ari Dekofsky, confirmed that agents responded to the airport that day but had found there to be no threat. “We determined that no further action was necessary,” she said on Saturday.

Mr. Makhzoomi was able to book a new flight on Delta Air Lines and arrived in Oakland eight hours after he originally planned. He said he has no plans to pursue legal action against Southwest Airlines but he does want the company to apologize for the way its employees treated him.

“My family and I have been through a lot and this is just another one of the experiences I have had,” he said. “Human dignity is the most valuable thing in the world, not money. If they apologized, maybe it would teach them to treat people equally.”

Courtesy New York Times