I agree with Anzel, it's most likely your form that's off and if you combine that with heavier weight it can cause low back issues. If you can have someone take a video of you doing squats. You could have a bad case of butt wink at the bottom of your lifts or you could be getting the bar to far forward and you're rounding your back on the way up. Only way you're going to know is to video it and break it down. You can find a lot of great squat videos on youtube that can help you analyize what you're doing wrong. Check out Mark Rippetoe's starting strength website, he's got a lot of great info on the squat.
Also as Anzel has said stretch your hamstrings and calves, they are very overlooked when it comes to lower back pain.
Don't give up on the squat unless you already have a messed up back, I have horrible knees and yet I squat every week and every rep is painful however....I still believe that as painful as they are I would've had to have my knees replaced years ago if I didn't do them!