We present a holographic method for defocus error compensation in tomographic phase microscopy, which enables high quality reconstruction in the presence of a meaningful run-out error of the measurement system. The proposed method involves indirect determination of the sample displacement from the in-focus plane. The sought quantity is deduced from the transverse movement of the rotating sample, which can be determined with high precision using correlationbased techniques. The proposed solution features improved accuracy and reduced computation time compared to the conventional autofocusing-based approach. The validity of the concept is experimentally demonstrated by tomographic reconstruction of an optical microtip.