Enhancement of oxygen ion conductivity in oxides is important for low-temperature (<500 °C) operation of solid oxide fuel cells, sensors and other ionotronic devices. While huge ion conductivity has been demonstrated in planar heterostructure films, there has been considerable debate over the origin of the conductivity enhancement, in part because of the difficulties of probing buried ion transport channels. Here we create a practical geometry for device miniaturization, consisting of highly crystalline micrometre-thick vertical nanocolumns of Sm-doped CeO2 embedded in supporting matrices of SrTiO3. The ionic conductivity is higher by one order of magnitude than plain Sm-doped CeO2 films. By using scanning probe microscopy, we show that the fast ion-conducting channels are not exclusively restricted to the interface but also are localized at the Sm-doped CeO2 nanopillars. This work offers a pathway to realize spatially localized fast ion transport in oxides of micrometre thickness.