Research on engineering geology at the PWRI dates back to the time when the Civil Engineering Laboratory (the predecessor of the PWRI) was established under the Ministry of Internal Affairs of Japan. At the time, the present Geology Team was called Division 4, and was engaged mainly in investigations and tests of road construction materials such as sand, gravel, and stone.

　When the Kamenose Landslide occurred in Osaka Prefecture in 1931, inflicting considerable damage on rivers and roads, countermeasures were taken using all civil engineering technologies then available. Before taking countermeasures, geological investigations were conducted systematically to understand the mechanism of landslide occurrence and select suitable techniques. This was a landmark achievement in the history of engineering geology.

　In 1938, seismic prospecting and electrical prospecting for bridge and dam foundations were implemented, which led to the use of various geophysical prospecting techniques in diverse civil engineering fields. In the same year, geological investigations for the Kanmon Roadway Tunnel connecting the islands of Honshu and Kyushu were commenced. This marked the start of not only a major era of geological investigations for roadway tunnels, but also the first step for engineering geology to become part of a major project. Then, in an organizational reform in 1939, Division 4 was renamed the Geological Test Division, and was later renamed the Geology Division in 1951.

　In the early 1950s, research on dam geology became active in line with the increase in the construction of high dams. The construction of arch dams beginning in around 1955 accelerated the development of dam geology together with rock mechanics which was being established at the time. On the other hand, geological investigations in preparation for two major road construction projects were initiated: one in 1958 for the Chuo Expressway and the other in 1959 for the Honshu-Shikoku Bridge Expressway. Meanwhile, due to an organizational restructuring that introduced a department-based system in 1958, the Geology Division, together with the Chemistry Division, was grouped into the Geology and Chemistry Department.

　In response to the dramatic increase in dam construction and shortage of favorable dam sites in around 1965, systematic investigation methods and technical classification and evaluation methods for ground geology were proposed in order to construct dams efficiently. In addition, in preparation for the Trans-Tokyo Bay Highway construction, many geological investigations of shallow sea areas and investigations and tests of soft rock were implemented. Research on geological disasters due to sediment hazards in the suburbs of large cities and erosion in coastal areas was also conducted.

　From around 1975, structures came to be built on various types of unfavorable ground, requiring more detailed, precise geological investigations. Research therefore focused on the mechanical and permeability properties of soft rock, methods for geologically classifying the bedrock composition, and methods for investigating the Quaternary fault, using new equipment and devices that the PWRI obtained upon moving to Tsukuba in 1979 pursuant to the government policy to transfer national research institutes to Tsukuba Science City. The durability and effective use of rock materials were also important research themes at the time.

　From around 1985, geophysical prospecting techniques were markedly improved, and tomography and other new geological investigation techniques were developed. On the other hand, there has been growing awareness of environmental conservation since the 1990s, and so civil engineering projects must now consider the environment as well. Meanwhile, with the organizational reform of the PWRI in 1996, the Geology Division was put under the Environment Department. In April 2001, the PWRI, which was under the Ministry of Construction (presently NILIM), made a new start as an Independent Administrative Institution (IAI) pursuant to the government policy to improve the management efficiency of national research institutes: the Geology Division became the Geology Team in the Material and Geotechnical Research Group at that time and later became the current Geology Research Team in the Geology and Geotechnical Engineering Research Group. Afterwards, Independent Administrative Institution PWRI changed into National Research and Development Agency PWRI in April, 2015.