If this thread was posted earlier I am truly sorry.
I was just thinking that the black metal that Pain has on his bodies sort of acts like the Frog Oil. It draws chakra forcibly into the body. It's possible that natural energy is animating the dead bodies and allows him to control them.
Just a thought, and yes I did think of a counter point "Well wouldn't Pa Frog of noticed the amount of energy being used" Good point, maybe he was so into battle that he didn't, LMAO.