Former world individual pursuit champion Phinney, who is now carving a successful career on the road with the BMC Racing team, claims the use of "finish bottles" is prevalent in the professional peloton.
The 22-year-old American told www.velonation.com: "There is widespread use of finish bottles, which are just bottles of crushed up caffeine pills and painkillers.
"That stuff can make you pretty loopy, and that is why I have never tried it. I don't even want to try it as I feel it dangerous.
"Another issue is taking something for an improvement, getting into that mentality. You have to ask why are you taking a painkiller?
"You are doing that to mask effects that riding a bike is going to have on your body - essentially, you are taking a painkiller to enhance your performance.
"But the whole reason we get into sport in the first place is to test our bodies, to test our limits. If you are taking something that is going to boost your performance, that is not exactly being true to yourself, not exactly being true to your sport."
The United States Anti-Doping Agency accused Armstrong's United States Postal Service team of running "the most sophisticated, professionalised and successful doping programme that sport has ever seen".
Armstrong, who won seven Tours de France between 1999 and 2005 and has always denied doping, declined the opportunity to co-operate with the USADA investigation.
Phinney, who finished fourth in the Olympic Games time-trial and road race, believes the opportunity should be taken to ensure cycling is whiter than white.
"They are just painkillers or anti-cramping pills or caffeine, but they are still pills - it is still a grey area in my mind," Phinney added.
"I feel like if you train with proper nutrition and proper hydration and if you race with proper nutrition and proper hydration, why do you need that stuff anyway?
"The way I see it, if we are going to turn the page, then why don't we write a whole new book? We can turn this sport into the absolute cleanest sport there is, if we do things right. So that is what I am trying to do."