I was going to fisk the Government's depressing sudden love affair with the discredited nonsense of "lie detectors", but I see the Ministry has already done it. Go and read; it's an instant classic. And as a bonus, there's a great comment from the Great Simpleton, who you occasionally find in comments here, about some effects of telecoms infrastructure on the welfare state.
It's certainly all nonsense - the 3G voice codec, AMR Narrowband, includes a band-pass filter between 200Hz and 3.4KHz, as do G711 and G729, so the markers VSA relies on, which are to be found between 8 and 12Hz, will be undetectable on any current mobile or fixed phone. Even the AMR Wideband high-quality voice standard will pass nothing - the band-pass for that one is 50Hz-7KHz. Any sound that does turn up at the VSA, therefore, is an artefact of some kind - a stray cosmic ray, or the acoustic echo cancellation at the local exchange going out of kilter when it produces the synthetic network noise to reassure you the line isn't dead. (You might be advised not to Skype the benefits office - they're considerably wider band when they are comprehensible at all.)
To expand on my comment over there, though, someone already markets a voice-stress analyser application for Windows Mobile smartphones. It's probably mostly witchcraft and social engineering, but it's very likely easier to do the opposite; either filter out the frequency band that is meant to be the marker, which could maybe sound weird or be too obvious if you could hear it at all, inject noise into that channel, or create a synthetic signal. That would be the hardest of the three to implement, but it would provide some interesting affordances - you could choose to sound more untrustworthy. If you could hear it, that is.
The only thing this achieves, then, is to deny some people their bennies entirely at random. Which is, of course, a highly political act.
Update: See here.