He graduated from the Medical School of Tokyo Imperial University in 1896.
He went to work at the Institute for the Study of Infectious Diseases under Dr. Kitasato Shibasaburō and an official at Quarantine Bureau. Took his doctorate (1906). Shiga became famous for the discovery of Shigella dysenteriae, the bacillus causing dysentery, in 1897, during a severe epidemic in which more than 90,000 cases were reported, with a mortality rate approaching 30%. The bacterium Shigella was thus named after him, as well as the Shiga toxin, which is produced by the bacterium.
After the discovery of Shigella, Shiga worked with Paul Ehrlich in Germany from 1901 to 1905. After returning to Japan, he resumed the study of infectious diseases with Dr. Kitasato. He became a professor at Keio University in 1920.
From 1929 to 1931, Shiga was the president of Keijō Imperial University in Keijo (Seoul) and was senior medical advisor to the Japanese Governor-General of Korea. Shiga was a recipient of the Order of Culture in 1944. He was also awarded the Order of the Sacred Treasure, 1st class, on his death in 1957.