Frequency-difference (FD) electrical impedance tomography (EIT) using a weighted voltage difference has recently been proposed for imaging haemorrhagic stroke, abdominal bleeding and tumors. Although its feasibility was demonstrated through two-dimensional numerical simulations and phantom experiments, we should validate the method in three-dimensional imaging objects. At the same time, we need to investigate its robustness against geometrical modeling errors in boundary shapes and electrode positions. We performed a validation study of the weighted FD method through three-dimensional numerical simulations and phantom experiments. Adopting hemispherical models and phantoms whose admittivity distributions change with frequency, we investigated the performance of the method to detect an anomaly. We found that the simple FD method fails to detect the anomaly, whereas reconstructed images using the weighted FD method clearly visualize the anomaly. The weighted FD method is robust against modeling errors of boundary-shape deformations and displaced electrode positions. We also found that the method is capable of detecting an anomaly surrounded by a shell-shaped obstacle simulating the skull. We propose the weighted FD method for future studies of animal and human experiments.