• Uncertainties of linear and volumetric wear were calculated for the on-machine measurements by Touch and Laser method. • There exists an optimal number of control intervals for re-estimation of the tool wear compensation factor. • For the values of linear wear below approximately 40 μm, the Laser system significantly better estimates the electrode wear compensation factor. • The electrode profile acquisition by the Laser method is highly recommended for the electrode diameters below approximately 20 μm. On-machine measurements play an important role in micro EDM milling. The measured tool electrode wear and the wear compensation have a strong influence on machining accuracy since the wear compensation methods require periodic measurements of the wear. The measurement uncertainties of the linear and volumetric wear measurements by the Touch and the Laser method were examined and results are presented in this paper. It was found that the linear wear measurements can be effectively performed by the Touch method when larger tool electrode diameters are used and sufficient machining is performed between the two control intervals, whereas the volumetric wear should be measured by the Laser method. To effectively compensate the tool electrode wear when tool electrodes with smaller diameters are used or low linear tool wear occurs between the two control intervals, the Laser method should be applied.