The current transport through Schottky contacts on wide band gap semiconductors GaN and SiC was studied on nanoscale by conductive atomic force microscopy. Two very different metal-semiconductor systems were investigated: i a uniform 5 nm thick Pt contact on GaN, and ii a discontinuous contact formed by self-assembled Au nanoclusters on SiC. The local current-voltage I-V measurements allowed to demonstrate the “laterally inhomogeneous” electrical behavior of the Pt/GaN contact, which was formed by a distribution of nanoscale patches with different barrier heights. This behavior was explained in terms of the inhomogeneities of the Pt/GaN interface and/or of the electrically active defects present in the GaN epilayer. The standard deviation of the local barrier height histogram was correlated with the dependence of the ideality factor n on temperature, deduced from conventional I-V measurements at variable temperatures on macroscopic Pt/GaN diodes. The local Schottky barrier height at the interface between the single metal nanoparticle and the semiconductor was determined in the system of self-assembled Au nanoclusters on SiC. The histogram of the Schottky barrier heights was measured on samples with different cluster size distributions and the dependence of the barrier height on the cluster size was demonstrated.