For a reliable evaluation of the geo-environmental risk due to naturally occurring asbestos (NOA) during rock excavation of large infrastructure projects, a proper procedure is needed. First, it is necessary to provide a detailed geological model tailored to the NOA-related issues that should drive the rock sampling procedures in order to obtain a representative sampling. The sampling procedures should take into account lithological variability and relative spatial distributions of the rock units. The geological model for NOA should be thus constrained by the main NOA petrofacies occurring in a given geotectonic context, which take into consideration both the mineralogical and structural features, and the identification of NOA homogeneous zones in which the NOA petrofacies are distributed. In this paper, some geo-environmental problems faced during the excavation, in meta-ophiolites, of a long highway tunnel are described. The geological model of the complex setting of the tunnel area (northern Italy, Alps-Apennines junction) is described, focusing on how the NOA-related problems were addressed to allow reliable and detailed estimations of NOA contents for each NOA homogeneous zone and the relevant tunnel layout segment.