Novel atomic structures on a H-terminated Si(100)-(2x1)-H surface were found using scanning tunneling microscopy (STM). The structures are distinguishable only from Si dimers in empty-state STM images. They were observed on arsenic- and phosphorus-doped substrates, but not on boron-doped substrates. Surface density of these structures was found to be proportional to the dopant density in the substrate. First-principles calculations clarify that they are consisting of dopant pairs that are segregated from the bulk material. Hydrogen atoms attached to the dopant pair are found to flip between two positions on the surface due to a quantum effect.