Japan Atomic Energy Agency (JAEA) has been conducting the environmental sample analysis, which is one of the IAEA's safeguards measures. In the analysis, isotope ratios of ultra-trace amounts of uranium and plutonium in samples taken from nuclear facilities are determined to detect undeclared nuclear materials and activities. In order to keep and enhance the reliability of the measurement results, validation of analytical methods and estimation of measurement uncertainty in such ultra-trace analysis should be properly done in accordance with worldwide standards. In this paper, the current activities on achievement of QA/QC (quality assurance and quality control) and estimation of measurement uncertainty in the ultra-trace analysis at a clean chemistry laboratory (CLEAR) of JAEA are reported.