The systematic quality assurance activities on documents of the safety assessment are required for the safety case of the low- and intermediate-level radioactive waste disposal facility. In this paper, quality assurance system focused on the input data including the site characterization, groundwater flow, system design and monitoring are prepared and discussed. Rule for the input data selection is suggested and applied for the safety assessment which is based on the in-situ/experiment observations, final facility design and waste pileup plan, engineered barrier, field monitoring, recent biosphere, and radionuclide inventory. The reduction of data uncertainty will be expected to contribute to the safety of disposal facility further.