The Parkinson vectors derived from 3-component geomagnetic data via the magnetic transfer function are discussed with respect to epicentre locations and hypocentre depths of 16 earthquakes (M ≥ 5.5) in Taiwan during a period of 2002–2005. To find out whether electric conductivity changes would happen particularly in the seismoactive depth ranges, i.e. in the vicinity of the earthquake foci, the frequency dependent penetration depth of the electromagnetic waves (skin effect) is taken into account. The background distributions involving the general conductivity structure and the coast effect at 20 particular depths are constructed using the Parkinson vectors during the entire study period. The background distributions are subtracted from the time-varying monitor distributions, which are computed using the Parkinson vectors within the 15-day moving window, to remove responses of the coast effect and underlying conductivity structure. Anomalous depth sections are identified by deviating distributions and agree with the hypocentre depths of 15 thrust and/or strike-slip earthquakes with only one exception of a normal fault event.