X-ray and electron diffraction measurements on the metal-insulator (M-I) transition compound PrRu$_4$P$_{12}$ have revealed the emergence of a periodic ordering of charge density around the Pr atoms. It is found that the ordering is associated with the onset of a low temperature insulator phase. These conclusions are supported by the facts that the space group of the crystal structure transforms from Im$bar{3}$ to Pm$bar{3}$ below the M-I transition temperature and also that the temperature dependence of the superlattice peaks in the insulator phase follows the squared BCS function. The M-I transition could be originated from the perfect nesting of the Fermi surface and/or the instability of the $f$ electrons.