Rapid urbanization has ledto increased construction of underground structures, requiring accurate evaluation of groundwater flow characteristics. The permeability coefficient is a key parameter governing groundwater flow. However, its accurate determination through laboratory testing is limited because of soil disturbance. Consequently, field permeability test results are widely used in design. This study quantifies the effects of soil disturbance and time-dependent clogging during borehole-based field permeability tests and proposes an improved field permeability testing method based on a bottom-water injection technique. Field tests were conducted under various ground conditions, including silty sand and weathered rock, and the results were analyzed in relation to injection methods and borehole conditions. The results show that the measured permeability coefficient varies significantly depending on the testing method and elapsed time, even under identical ground conditions. In silty sand, the upper-water injection method yielded permeability coefficients ranging from approximately 2.66 × 10⁻³ to 4.30 × 10⁻³ cm/s, showing a decreasing trend over time because of progressive clogging. In contrast, the bottom-water injection method produced higher permeability coefficients (approximately 3.87 × 10⁻³ to 7.85 × 10⁻³ cm/s) with reduced variability, indicating that clogging effects were effectively mitigated. However, the measured permeability coefficient is highly dependent on testing conditions and may not directly represent intrinsic soil properties. These findings suggest that conventional field permeability tests may significantly underestimate in situ permeability because of clogging effects, and that the proposed bottom-water injection method provides a more stable and representative evaluation under field conditions.