We studied the electron transport properties of micrometre-sized all-Al tunnel junctions (TJs) between 2 and 300 K, in which the AlOx layer grown by O2 plasma was moderately Ar-ion-milled prior to top electrode deposition. In contrast to the direct tunnelling in the TJs whose barriers are intact (not ion-milled), the zero-bias conductances and the current-voltage characteristics of the TJs as processed are found to be best described by the fluctuation-induced tunnelling conduction mechanism. This observation indicates the formation of nanoscopic incomplete pinholes in the AlOx layer, owing to large junction-barrier interfacial roughness introduced by the ion-milling process. Topographical features revealed by the cross-sectional transmission electron microscopy imaging of the TJ stack conform to this result. This study is of relevance to cases in which ion-milling techniques are applied in tailoring the TJ properties.