Check her for redness, swelling or any kind of irritation or even discharge. Little girls can get yeast infection brought on by damp clothing, antibiotics etc just like adults. She may need to be seen by a doctor. I can even be a laundry detergent being the villan, or the material her panties are made out of. It is natural for that age of children to touch themselves but if she is telling you she is bothered then I would take a trip to the pediatrician.
I agree with you that it isnt masturbation , it sounds like there is an irritation there so check out if she is using the bathroom a lot maybe a small bladder infection going on ,it is well known children do not wipe well so you may want to have a light and easy chat with her , about how she wipes ,also have her urine tested for any infection that is easily treated ...Ask her does it itch, hurt in that area , ...Good luck