Qena-Safaga road, which is one of the vital transportation lines in south of Egypt, is affected by a set of recent NE-SW to ENE-WSW vertical tensile and en echelon fractures. These fractures are distributed for about 12 km along both sides of the road and constitute a major threat to the infrastructure and environment. Some studies suggested the tectonic origin of these fractures while others suggested that they were formed due to geotechnical problems in the shallow subsurface soil. In order to study the nature and distribution of these fractures in the subsurface, low cost seismic surveys were conducted at the area of KM 22 of Qena-Safaga road. Eleven shallow seismic refraction lines as well as three MASW lines were acquired. The seismic refraction data were analyzed using tomographic methods to produce 2D velocity-depth models. To estimate the near surface seismic properties such as Vp/Vs and Poisson’s ratio that are important for the geologic interpretation of the data, MASW data where analyzed to obtain 1D shear wave velocity models. 3D images including 3D volume, fence diagram and depth slices were also produced to study the vertical and lateral variation of the P-wave velocity. In the resulted 2D tomographic models, three seismic units were deduced. The first unit represents the thin weathered surface layer having P-wave velocities of 300–700 m/s. The second unit has P-wave velocities of 700–1600 m/s and S-wave velocities of 281–926 m/s. It may represent the marl unit of Pliocene Durri Formation. Its thickness ranges from 11.8 m to 30 m. The bedrock was deduced to be at depths from 13 to 40 m and is characterized by velocities greater than 1600 m/s. The fractures were traced down to the bedrock along the seismic sections. The variable thickness of the marl unit as well as the variable depths of the bedrock were deduced to be resulting from the effect of subsurface.