The crystal structure of lithium ion conductors, Li3Sc2(PO4)(3) and Li3-2x(Sc1-xMx)(2)(PO4)(3) (M = Ti, Zr) with x = 0.10, were refined by Rietveld analysis for neutron diffraction patterns in order to confirm the site location and site occupancy for Li ions. The Rietveld refinement confirmed that a high disorder was introduced to three kinds of Li sites in the high temperature superionic conduction phase of Li3Sc2(PO4)(3). The high temperature phase was stabilized at room temperature by substituting Ti4+ or Zr4+ for Sc3+ sites. The stabilized materials were also found to have similar high disorder over the Li sites.