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Transportation spokesman Bill Adams said Friday evening that the department hadn’t received CAIR’s complaint but that it “thoroughly investigates every complaint it receives involving discrimination.”

AirTran said it regrets the incident escalated to the heightened security level, but said that it complied with all Transportation Security Administration, Homeland Security and law enforcement directives and had no discretion in the matter.

“We sincerely regret that the passengers on Flight 175 did not have a positive travel experience,” the airline said in a statement released Friday. “We trust everyone understands that the security and the safety of our passengers is paramount and cannot be compromised.”

TSA said the passengers who alerted the flight crew to what they considered a suspicious remark, as well as the crew, acted responsibly.

“TSA counts a vigilant traveling public as an important layer of security and continues to encourage passengers to be alert and report suspicious activity,” the agency said.

AirTran refunded the fares of the passengers who were removed from the flight and said it would reimburse them for expenses incurred by taking another airline. It also has offered to pay for their return passage to Washington.

But CAIR said the airline overreacted and called booting all nine Muslims off the plane inexcusable.

“If one person made a remark that somebody thought was suspicious, why were nine people kept off the flight?” Mr. Hooper said.