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It's my right hand pinky, ring finger and middle finger. Also the palm of hand below fingers.
Read a lot of people can have this issue, and even had it myself. Really, the correct way to hold the camera is to have your left hand support the camera's weight while you mess with the controls, shutter, and balancing with the right. I was subconsciously holding almost all the weight with my right hand when I first started out with DSLRs, and it hurt after a while in the same places, plus my wrist.
Holding the camera the correct way solved this problem. Also, between shots, I'll hold the camera by the lens near the mount, which uses mostly my thumb, index finger, and upper palm. This lets the other half of my hand rest. Even though they don't hurt anymore, those parts will still get fatigued after a while if you're constantly using them.
I'd seriously consider not using camera with the strap single handedly, since the technique is hurting your hand. Either that, or maybe get one of those hand straps that keeps your hand pressed to the camera:
That way, you don't need as serious a grip on the camera as you pull it up and when you carry it (really don't need much of a grip at all).