American Airlines said it prevented the agent from flying because of discrepancies in the standard paperwork he filled out identifying himself as an armed law enforcement officer. The airline denied the decision was related to his ethnicity.
The incident revived questions about racial profiling by airlines after the Sept. 11 attacks, in which more than 3,000 people died when 19 men of Arab descent hijacked four commercial aircraft and crashed them into the World Trade Center in New York, the Pentagon outside Washington and a field in Pennsylvania.
The agent, who was not identified by the Secret Service, was to fly from Baltimore Washington International Airport to Dallas to protect Mr. Bush on vacation at his ranch in Crawford, Texas. He was carrying a weapon because he was on official duty.
The agent's first flight was canceled, forcing him to book himself on a second flight and to fill out the paperwork, which is standard for armed federal, state and local law enforcement officers flying on official business, a second time.
After boarding, the agent was asked to get off the plane for more security checks and ultimately was barred from taking the Tuesday flight.
Ibrahim Hooper of the Council on American-Islamic Relations said the agent told him he felt he had been kicked off the Baltimore-to-Dallas flight because of his religion and ethnicity.
But American Airlines spokesman Todd Burke said: "This has absolutely nothing to do with ethnicity of the agent. What this has to do with this was confirming that an armed individual was indeed who he said he was."
The agent eventually traveled to Dallas on an American flight on Wednesday. He asked that his name not be released for security reasons.
"We certainly apologize to the agent for any inconvenience," Burke said. "But during this time of heightened security, we feel no one is above the approved security procedures."
Hooper said the group has written a letter to the airline asking for a clarification of its rules regarding "racial and ethnic discrimination."
The Secret Service is conducting an inquiry into the incident, said spokesman Jim Mackin.
Federal agents regularly travel armed aboard commercial flights, law enforcement officials said Thursday, and there is a routine procedure to ensure safety.
Before boarding a plane armed, advance notice to the airline is given and an agent goes through several credential and identification checks. Once through security, the armed agent's seat assignment is noted on the flight manifest for the crew's knowledge.
In addition, it is routine procedure fr any armed agents to introduce themselves to the pilot or co-pilot upon boarding the plane.
FBI spokesman Pete Gullota said a similar incident occurred shortly after the Sept. 11 terrorist attacks.
Gullota said an armed, off-duty FBI agent from the Baltimore office was not allowed to board a plane by a pilot despite following the security procedures for armed agents. Gullota refused to identify the airline but said the issue was cleared up and resulted in the pilot's suspension.
"This, unfortunately, is not the first time something like that has happened," Gullota said. "In most instances the airlines are very happy to have us on-board. We don't just don't show up at gate armed. We go through routine and a whole lot of people are notified."
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