You might want to check your form. Your knees should stay behind your toes if that makes sense. Also, you should be bringing your butt back and out and sitting back, with your chest up. I think squats done properly should not cause back pain. Hth! Gl!
Oh and I'm not a squats expert but I have a really good body pump instructor at my gym who stresses good form and that's what she says for squats and I never have a problem.