Abstract Permeability of geomaterials is the most important parameter involved in the assessment of advection of groundwater and contaminants in the subsurface and for the design of barriers to contain hazardous wastes. Evaluation of the permeability of soils by employing a geotechnical centrifuge, where centrifugal acceleration is used to simulate the prototype conditions, is an area of current research interest. This paper presents a working methodology that can be employed for measuring the hydraulic conductivity of compacted fine-grained soils in a geotechnical centrifuge. Two different hydraulic conductivity setups have been developed for silty sand and clays. The paper also studies the effect of sample length, the limiting acceleration levels, and the time of centrifugation on the hydraulic conductivity measurements.