We have proposed virtual-phase-conjugation-based optical tomography (VPC-OT) using a virtual phase conjugation technology for single-shot and three-dimensional optical tomography. In VPC-OT, a random-spatial-phase-modulated probe beam is irradiated to the sample to be measured, and the complex amplitude of the signal composed of a superimposition of light reflected from each layer of the sample is measured. A three-dimensional tomogram of intensity and phase is obtained by reproducing the measured complex amplitude using a phase conjugate wave in a virtual optical system built in a computer. At this time, by changing the parameters of the virtual optical system, it becomes possible to obtain information of various tomographic planes from the data obtained with a single measurement. In the ideal virtual phase conjugate reproduction process, free space propagation can be assumed; however, in the actual measurement, due to the distortion of the waves and the surroundings of the sample to be measured, a mismatch will occur in modulation and demodulation, and the separation accuracy between different tomographic planes would be degraded. We perform an experiment to clarify the characteristics of VPC-OT in this situation. In this experiment, three-dimensional optical tomography is performed using an etching glass having a periodic structure of 30 μm as a sample, and the phase distribution is measured quantitatively. Furthermore, by placing a cover glass in front of the object and performing the same measurement, we discuss the characteristics and performance of VPC-OT when there is an optical distortion around the sample to be measured.