Having second thoughts about those new full-body scanners being used at airports by the Transportation Security Administration? The federal agency charged with protecting the nation’s transportation systems may want to take a second look — at you.

It apparently did when Karen Cummings refused to submit to a scan, which uses high-frequency radio waves to see through your clothes. Cummings, who works for a software company in Boston, described what subsequently happened to her at Logan Airport as “unnecessary” and “unpleasant.”

“The pat-down was completely thorough, as though I was a common criminal or a drug pusher,” she said. “The only place I was not touched was in my crotch — and isn’t that the one place they should be checking, after the underwear bomber?”

Cummings is part of a small but growing group of air travelers who say that they’re troubled by the TSA’s use of advanced imaging technology.

Last fall, the agency began installing 150 new scanners (including at Reagan National and BWI Marshall), and it plans to deploy an additional 450 this year. Some passengers are worried about the intrusive nature of the electronic searches, while others have voiced concerns about possible exposure to harmful radiation. (Experts say radiation levels are very low.)

Screening by a full-body scanner is optional for all passengers, according to the TSA. “Those who opt out may request alternative screening at the checkpoint, to include a pat-down,” said Greg Soule, an agency spokesman. Although he declined to offer details on the agency’s screening techniques, he added that checkpoint requirements for passengers departing from the United States haven’t changed since the underwear bomber incident last December. In other words, the TSA claims it isn’t pushing travelers into the scanners and punishing those who decline a scan.

But Cummings and others say they don’t feel as if they have a real choice.

“The additional screening makes you want to go through the scanner, as it is so much more impersonal in the long run,” she told me.

And her experience is hardly an isolated one. Houston-based Web developer Cheryl Wise had a similar confrontation when she refused to be scanned in Denver earlier this year. A TSA screener, who she says was upset by her decision, ordered a “level two” search of her luggage.

“Every compartment of my computer bag was opened and every pocket emptied,” she recalled. “Every compartment or pocket of my computer bag that held an electronic device was wiped separately with an explosives detector, as were my shoes and the inside of my purse that held no electronics at all.” Wise published the entire account on her blog, by-expression.com, under the headline, “TSA screening insanity.”

The TSA has its own blog, of course, which it uses to counter any claims that it has gotten carried away with its tech toys. In a recent post, it praised the full-body scanners, pointing out that since last year, agents had found such items as a pocket knife hidden on someone’s back and a syringe full of liquid concealed in a passenger’s underwear. “These finds demonstrate that imaging technology is very effective at detecting anomalies and can help TSA detect evolving threats to keep our skies safe,” the agency said.

My first instinct was to dismiss the traveler complaints as cases of a few TSA officers being overly vigilant at a time when security has been heightened and when the agency is trying to prove the value of the scanners, which cost $130,000 to $170,000 per unit. But security guru Bruce Schneier told me that he’d heard “lots of anecdotes” about extra screening, too.

And then I went through one of the machines myself, a few weeks ago in Salt Lake City. After I passed through a magnetometer, I was ushered into a large device that looks a little like the teleporter from the Jeff Goldblum version of “The Fly,” asked to empty my pockets and hold my hands above my head.

I admit, the scan felt somewhat invasive, with me holding my hands in the air as if I were an apprehended fugitive. The widely circulated pictures of scanned people — every contour of their bodies visible and their faces electronically airbrushed away — didn’t make me feel any better. Were the hidden pocket knives and syringes filled with liquid worth all this? And what was in that syringe that the TSA confiscated, anyway?

I asked other travelers about their experiences with refusing to use the devices, but I could find no hard evidence that screening dissidents were being penalized in a systematic way.

“I respectfully decline to go through the body scan,” reader Phil Kipnis said he told a TSA officer in San Francisco recently. The officer appeared “startled,” according to Kipnis. Then he pointed Kipnis, a Santa Clara, Calif., business owner, to the secondary screening area.

“A male TSA employee shook his head and ran the wand over my torso and told me to collect my things and turned back to watch the other passengers,” he said.

I believe the TSA when it says that it has no formal policy of punishing passengers who don’t want to go through the full-body scanners. But it doesn’t need one. Just a few stories of overly watchful officers giving people a thorough once-over if they refuse may be enough to persuade reluctant air travelers to submit to a virtual strip-search. And all it needs to reinforce those fears is an occasional shake of the head.