The Tsugaru Strait has eastern and western necks, both approximately 20 kilometres across. Initial surveys undertaken in 1946 indicated that the eastern neck was up to 200 metres deep with volcanic geology. The western neck had a maximum depth of 140 metres and geology consisting mostly of sedimentary rocks of the Neogene period. The western neck was selected, with its conditions considered favourable for tunnelling.
Geology of the undersea portion of the tunnel consists of volcanic rock, pyroclastic rock, and sedimentary rock of the late Tertiary era. The area is folded into a nearly vertical anticline, which means that the youngest rock is in the centre of the Strait, and encountered last. Divided roughly into thirds, the Honsh? side consists of volcanic rocks (andesite, basalt etc); the Hokkaid? side consists of sedimentary rocks (Tertiary period tuff, mudstone, etc); and the centre portion consists of Kuromatsunai strata (Tertiary period sand-like mudstone). Igneous intrusions and faults caused crushing of the rock and complicated the tunnelling procedures.
Initial geological investigation occurred from 1946–1963 which involved drilling the sea-bed, sonic surveys, submarine boring, observations using a mini-submarine, and seismic and magnetic surveys. To establish a greater understanding, a horizontal pilot boring was undertaken along the line of both the service and pilot tunnels
Tunnelling occurred simultaneously from both the northern and southern ends. The dry land portions were tackled with traditional mountain tunnelling techniques, with a single main tunnel. However, for the 23.3-kilometre undersea portion, three bores were excavated with increasing diameters respectively: an initial pilot tunnel, a service tunnel, and finally the main tunnel. The service tunnel was periodically connected to the main tunnel with a series of connecting shafts, at 600- to 1,000-metre intervals. The pilot tunnel serves as the service tunnel for the central five-kilometre portion.
Beneath the Tsugaru Strait, the use of a tunnel boring machine (TBM) was abandoned after less than two kilometres owing to the variable nature of the rock and difficulty in accessing the face for advanced grouting. Blasting with dynamite and mechanical picking were then used to excavate.