In 1986, while seeking to observe the sharks, Kihachiro Aratake, a director of the Yonaguni-Cho Tourism Association, noticed some seabed formations resembling architectural structures.

[5][6] It is composed of medium to very fine sandstones and mudstones of the Lower Miocene Yaeyama Group believed to have been deposited about 20 million years ago.

[9] German geologist Wolf Wichmann, who studied the formations in 1999 during an expedition organized by Spiegel TV, and in 2001 by invitation of Graham Hancock, concluded that they could have been formed by natural processes.

Robert Schoch, as well as Patrick D. Nunn, Professor of Oceanic Geoscience at the University of the South Pacific, note that the formations are purely natural.

[12] In 2019, Takayuki Ogata and other researchers conducted a topographical analysis of Yonaguni Island using a digital elevation model and geological field investigations of the strata, rocks, and microtopography of outcrops at three locations, known as "geosites", Tindabana, Kube Ryofurishi, and Sanninudai.

As a result of their research, they noted that although Yonaguni Monument may look like an artificial construction, it is a natural feature formed by the weathering and erosional processes acting on bedding and linear joints in sandstone.

[11] They also point to the relative absence of loose blocks on the flat areas of the formation, which would be expected if they were formed solely by natural erosion and fracturing.