An American Airlines pilot refused to fly an armed Secret Service agent partly because the Arab-American agent became loud and abusive after his identity was questioned, the airline said Thursday.

The airline called claims by the agent and his lawyers that he was a victim of racial or ethnic profiling "frivolous."

"American will not allow any armed individual onboard, regardless of who he or she is, if that person is angry or acting in a manner that the crew believes could jeopardize the safety of the flight," the airline said in a written statement.

The agent, whose name was not released but who was identified by the Weekly Standard magazine as Wallid Shatter, claims he was booted off an American Airlines flight between Baltimore and Dallas on Christmas day. Shatter was en route to Texas to join President Bush's security detail.

The pilot of the flight said Shatter was removed for being abusive and "unprofessional," not because of his ethnicity.

Armed federal agents must submit paperwork and meet other strict requirements before flying on commercial flights, including meeting the pilot and co-pilot. Shatter did so, his attorneys contend, but was then moved to American Airlines Flight 363 after his original flight was grounded by mechanical failures.

At that time, his paperwork was crossed out and re-written by a ticketing agent. He was still permitted to board, and briefly met the pilot, but shortly thereafter was removed for further security clearances, along with a few other passengers of "Pakistani and Indian descent."

"I don't think there's any doubt that this incident would not have occurred if this agent was not an American of Arab descent. We feel that the pilot was unable to see past the agent's ethnicity and that his biased and stereotyped view made innocuous and innocent facts seem suspicious in his eyes," said attorney Christy Lopez, who is representing Shatter.

The Secret Service is investigating the dispute. An inspector is interviewing people involved and sources cannot say when the review will be complete.

One source near the Secret Service said the pilot has indeed called the Secret Service to complain about the agent, saying he acted unprofessionally, but it is not clear whether the pilot has filed a formal complaint or not.

According to a release from American Airlines, the pilot said the flight attendants "were concerned about the actions" of the passenger and that his paperwork "was unreadable because it was a carbon copy and there were missing items."

After an hour and a half delay, the pilot said the agent asked him what the problem was, to which he replied, "This was an American Airlines issue and none of his concern at this time."

The pilot said that at that point, "The individual became very hostile with me." He also claimed that "the police agreed with me that there was legitimate concern because of his unprofessional behavior."

Lopez, who was joined by attorneys John Relman and Kristi Ellis, said that the pilot's report is "completely false" and only made to justify "post hoc rationalizations" to excuse his behavior.  President Bush said before the new year that he would be "madder than heck" if the accusations of ethnic profiling were true.

Lopez also disputed a report by a flight attendant who said she found a book written in Arabic on the agent's seat. Relman denied the charge, saying the agent doesn't even read or write Arabic and called the story a "blatant lie."

Lopez said the agent does not intend to sue, but wants some changes made.

"His interest is simply in seeing that procedures are put in place so that he and others similarly situated do not have to go through this sort of ordeal unnecessarily in the future."

Fox News' Jim Angle, Courtney Wells and the Associated Press contributed to this report.