High resolution inductively coupled plasma mass spectrometry coupled with an on-line flow injection system (FI-HR-ICP-MS) was applied to determine the ultra-trace level 99Tc in soil. The flow injection system (PrepLab) was composed of two TEVA-SpecÒresins, reduced remarkably the sample amounts and the analysis time, compared to the conventional analytical methods. In the flow injection system, Mo and Ru were sufficiently eliminated by using the flow injection system, with the decontamination factors of 1.6.104 and 9.9.105, respectively. With the present method, it was possible to determine ultra-low level of 99Tc in 3-6 g soil at 3–5 hours of analysis time per sample. The relative standard deviation for each sample was less than 4%. The detection limits for 99Tc was 85 fg.ml–1 (0.05 mBq.ml–1), which was calculated from the three times standard deviation of the count rate of the blank.