Flysch formations are generally characterised by evident heterogeneity in the presence of low strength and tectonically disturbed structures. The complexity of these geological materials demands a more specialized geoengineering characterisation. In this regard, the paper tries to discuss the standardization of the engineering geological characteristics, the assessment of the behaviour in underground excavations, and the instructions–guidelines for the primary support measures for flysch layer qualitatively. In order to investigate the properties of flysch rock mass, 12 tunnels of Egnatia Highway, constructed in Northern Greece, were examined considering the data obtained from the design and construction records. Flysch formations are classified thereafter in 11 rock mass types (I–XI), according to the siltstone–sandstone proportion and their tectonic disturbance. A special geological strength index (GSI) chart for heterogeneous rock masses is used and a range of geotechnical parameters for every flysch type is presented. Standardization tunnel behaviour for every rock mass type of flysch is also presented, based on its site-specific geotechnical characteristics such as structure, intact rock strength, persistence and complexity of discontinuities. Flysch, depending on its types, can be stable even under noticeable overburden depth, and exhibit wedge sliding and wider chimney type failures or cause serious deformation even under thin cover. Squeezing can be observed under high overburden depth. The magnitude of squeezing and tunnel support requirements are also discussed for various flysch rock mass types under different overburdens. Detailed principles and guidelines for selecting immediate support measures are proposed based on the principal tunnel behaviour mode and the experiences obtained from these 12 tunnels. Finally, the cost for tunnel support from these experiences is also presented.