Whole body counters (WBCs) are used to monitor radiation workers for internal contamination of radionuclides at domestic nuclear power plants (NPPs). A WBC is a scintillation detector using sodium iodide (NaI) and provides the identification of inhaled radionuclide and the measurement of its internal radioactivity in a short time. However, it is often possible to estimate external contamination as internal contamination due to radionuclides attached to the skin of radiation workers and this leads to an excessively conservative estimation of radioactive contamination. In this study, several experiments using a WBC and the Korean humanoid phantom were performed to suggest the more systematic method of discrimination between external and internal contamination. Furthermore, a WBC geometry experiment was conducted to suggest the optimal WBC geometry in consideration of deposited areas inside the body for dominant radionuclides at NPPs. The procedure of measurement and estimation of internal radioactivity for radiation workers at NPPs was improved on the basis of experimental results. Thus, it is expected to prevent from estimating internal exposure dose conservatively owing to the application of accurate whole body counting program to NPPs.