The Department of Homeland Security is facing a legal challenge from the American Civil Liberties Union over the treatment of a passenger at John F. Kennedy International Airport in the days after a major terrorism alert.

The passenger, who was born in Iraq, was forced to cover up Arabic script on his T-shirt before he was permitted to board a JetBlue flight last year, according to a complaint filed in U.S. District Court in Manhattan yesterday.

The lawsuit could clarify the limits of the discretion of airline and law enforcement officials to refuse to allow customers to fly. The issue also is being litigated in U.S. District Court in St. Paul, Minn., where six Muslim imams claim they were arrested and removed from an America West flight for praying in public before boarding.

In the New York case, the passenger, Raed Jarrar, was finally permitted to board his flight to Oakland, but only after he consented to wearing a different T-shirt, one purchased for him at an airport gift shop by a JetBlue employee, the complaint says.

Mr. Jarrar’s original T-shirt bore a slogan, “We Will Not Be Silent,” in both English and Arabic. The slogan was first used by an anti-Nazi student group in Germany, the complaint said.

“All he was doing was being himself and wearing his T-shirt with Arabic writing,” Mr. Jarrar’s lawyer, Aden Fine of the ACLU, said in an interview. “He didn’t do anything that could possibly be construed as suspicious.”

It was not so much the content of the message that troubled airline officials but the Arabic lettering, the complaint alleges. While waiting to board the flight, according to the complaint, Mr. Jarrar was told by a Transportation Security Administration official that “it was impermissible to wear a shirt with Arabic script at an airport.” The complaint identifies the official only as “Inspector Harris.”

The T-shirt that JetBlue supplied displayed the slogan “All Original New York Authentic Brand,” according to the complaint.

The incident occurred in August 2006, days after British law enforcement officials announced they had disrupted a plot to blow up trans-Atlantic flights.

“JetBlue has no policy regarding apparel or messages on apparel,” an airline spokesman, Bryan Baldwin, said. He declined to comment on the suit. The company, listed as a defendant, is accused of violating Mr. Jarrar’s civil rights. The official at the Transportation Security Administration, a division of the Department of Homeland Security, is accused of violating Mr. Jarrar’s First Amendment rights. A spokeswoman for the TSA declined to respond to a series of questions submitted by e-mail.

Mr. Jarrar, 29, lives in Washington, D.C. He emigrated from Iraq in 2005, Mr. Fine said. An architect by training, Mr. Jarrar is currently employed as an Iraq analyst for a Quaker organization, the American Friends Service Committee, which is devoted to assisting civilian victims of war, according to the organization’s Web site.