In 1928 Ishihari was appointed commander of the Kwantung Army and took part in the invasion of Manchuria in 1931. The following year he was promoted to the rank of colonel he was a member of the Japanese delegation to the League of Nations that walked out in protest after the Lytton Commission report was critical of the country's role in Manchuria.
Ishihari worked as a section chief in the Operations Bureau in Tokyo. He became chief of operations in March 1937 but was demoted after arguing against Japanese expansionist foreign policy. Ishihari retired from the Japanese Army in December 1938.
In August 1945, Naruhiko Higashikuni, the head of the surrender government, appointed him as a special military adviser. He now controversially attacked Hideki Tojo and other former Japanese political and military leaders as war criminals. Kanji Ishihari died in 1949.