Transportation Security Administration chief John Pistole on Monday said he feared a proposed Wednesday protest of new airport screening policies will clog already long security lines and risk delays and missed flights for passengers on one of the busiest travel days of the year.
But he added he understands the public's concerns about privacy issues regarding new airport body scan machines.
"One of the great things about America is people can protest, they can do things they want to bring attention to," Mr. Pistole told reporters at a breakfast sponsored by the Christian Science Monitor.
"My real concern for this is for the vast majority of travelers who are simply trying to get home to be with love ones for the holiday. If they miss a flight because of a group of people are blocking access or taking extended periods of time, I feel bad for those people who would not be protesting."
A loosely organized "National Opt-Out Day" boycott of body scans is planned to coincide with the Thanksgiving holiday travel rush. Protest organizers are asking passenger to refuse the body scans and instead request a full manual "pat-down" by a security official.
Body scans take as little as 10 seconds, but people who decline the process must submit to a full pat-down, which takes much longer. That could cause a domino effect of delays at airports nationwide.
Mr. Pistole said of the 34 million airline travelers since the new security messages were instituted Nov. 1, only a small percentage have been subjected to pat-downs.
"Pat-downs are a secondary screening tool," he said. "It seems like the media has been reporting on all these pat-downs as if everybody has been patted down.
The TSA chief promised that the nation's airports would be fully staffed with security personal during the Thanksgiving holiday travel period this week, when 20 million passengers are expected.
The Obama administration has had trouble coordinating its message on the controversial policy.
On Sunday, Secretary of State Hillary Clinton said on NBC's "Meet the Press" that she thought "everyone, including our security experts, are looking for ways to diminish the impact on the traveling public."
She was followed by Mr. Pistole who said on CNN's "State of the Union," that his agency was looking for ways to diminish the impact of the invasive screening, but "we're not changing the policies."
Then he released a statement later in that day saying the agency would try to make screening "as minimally invasive as possible."
• Joseph Weber contributed to this report.
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