I'm a government contractor who is required to have high security clearances. Every 5 years we are expected to undergo our "re-poly". I think they require re-polys to keep our lifestyles honest as we age. So that people don't get in clean and then get dirty after the fact. My beef is with the whole polygraph "test" in general.
Whenever I have a poly coming up, I run the gamut of emotions:

annoyed, embarrassed - that our government feels this is a cost-effective deterrent of dishonesty

scared, distressed - that my job rests on my passing a "test" orchestrated not by science but by trickery, all with the pressure(anxiety-inducing) of losing my entire income based on an outcome that is dependant on how calm, non-anxious I can be.
This site:
antipolygraph.orgoutlines the facts surrounding the claim that POLYGRAPHS JUST DON'T WORK. Honest people get fingered out by polygraphs every day. And spies pass polygraphs just as often. The book "The Lie Behind the Lie Detector" is a free publication that is available to all people who need to "pass" a polygraph "test".
Our own government knows that foreign spies are trained to beat polygraphs, just like we teach our own spies how to beat polygraphs. So why all the farce? They know it is ineffective. I spent 5 hours at my last polygraph. I was being paid with government contractor dollars, and the polygrapher was also being paid with government dollars (AKA TAX DOLLARS). And 5 hours isn't unusual.
Not only are tons of tax dollars being used to pay people to give and receive these arbitrary ordeals, but tax dollars are used to send polygraphers to training for these unscientific, ineffective "tests".
I agree whole-heartedly that we need to screen employees with access to sensitive information in the interest of national security. But there must be a better way. If there isn't a better way, that does not justify wasting money on an ineffective way.
Just because the threat of having to take a polygraph might discourage dishonest people from applying; it does not prevent MOTIVATED, EDUCATED dishonest people from applying. Is the cost really worth the protection? Would you spend a million dollars on a water filter that only removed dirt from the drinking supply, but let microscopic bacteria through?
Should the government continue to waste tax payer dollars in the hopes of discouraging petty liars, but without the guarantee that they are filtering out serious liars? Also, with the added consequence of losing qualified, often talented, honest people who can't calm themselves during a polygraph? Can we think of a better way?