Archaeological evidence for wind musical instruments made by modern humans has been well established from the Upper Palaeolithic in Europe. Musical instruments evidently made by Neanderthals have not been found so far. The most controversial object is a juvenile cave bear femur with two complete holes, found in 1995 in the Middle Palaeolithic layers of the Cave Divje babe I, Slovenia. The bone was interpreted as a possible Neanderthal ‘flute’, but some scholars have firmly rejected this hypothesis on the basis of taphonomic observations, suggesting a carnivore origin for the holes. Here, we show the results of X-ray computed micro-tomography (mCT) performed on the Divje babe I ‘flute’. Our analyses demonstrate that there were originally four holes, possibly made with pointed stones and bone tools. Most surface modifications near the holes, previously interpreted as effects of carnivore gnawing, are post-depositional marks. Furthermore, a thin layer has been removed around one of the complete holes, producing a flat surface, possibly to facilitate perforation. The new data show that a Neanderthal manufacture of the object cannot be ruled out.