Paul was escorted out of the airport security area in Nashville, Tennessee, by local authorities after he declined to agree to a physical patdown, the Transportation Security Administration said in a statement.
Paul missed his flight to Washington, but TSA, which handles security screening at U.S. airports, denied claims by the senator's office that he was detained.
The TSA did not say what triggered the alarm and said Paul was booked on another flight and rescreened without incident.
Transportation security officials have been sharply criticized by passengers, consumer groups and members of Congress for screening policies that critics say violate personal privacy.
The agency defends its procedures, which they say are needed to ensure passenger safety.
Paul has criticized TSA searches as random and not based on threat analysis, and has confronted agency officials about screening complaints from travelers in his Kentucky district.
He has recommended that authorities eliminate pat downs as part of everyday security, saying TSA should more heavily emphasize non-invasive methods for assessing risk.
Paul has said close screening of members of Congress and other frequent fliers known to airlines and security officials is a poor use of security resources.
Ron Paul, a U.S. congressman and Republican presidential hopeful, tweeted that his son was being detained for refusing a full-body pat-down "after anomaly in body scanner."
(Reporting By Thomas Ferraro and John Crawley; Editing by Jackie Frank)
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