The Imperial General Staff Headquarters was completely independent of the civilian government of the Empire of Japan, including the Cabinet and even the Prime Minister of Japan. Prime Minister Ito Hirobumi was allowed to attend meetings by the express order of Emperor Meiji during the First Sino-Japanese War. However, Prime Minister Katsura Taro, despite his military background, was denied entry to meetings during the subsequent Russo-Japanese War.
Imperial Decree 658 of 18 November 1937 abolished the original Imperial General Headquarters, which was then immediately re-constituted under Military Decree 1, which gave the new Imperial General Headquarters command authority over all military operations during peacetime situations as well as wartime situations. In November 1937, to bring the chiefs of Army and Navy General Staff into closer consultation with his government, Emperor Hirohito established a body known as the Imperial General Headquarters-Government Liaison Conference within Imperial General Headquarters. The Liaison Conferences were intended to assist in integrating the decisions and needs of the two military sections of Imperial General Headquarters with the resources and policies of the rest of the government. Reaching agreement between the Army and Navy on strategic planning was often difficult. When agreement was finally reached on an important strategic issue, the agreement was reduced to writing in a document called a Central Agreement and signed by both Chiefs of Army and Navy General Staffs.
The final decisions of Liaison Conferences were formally disclosed and approved at Imperial Conferences over which Emperor Hirohito presided in person at the Tokyo Imperial Palace.
During the Pacific War, and after the firebombing of Tokyo, the Imperial General Headquarters relocated to an underground facility in the mountains outside of Nagano.
With the surrender of Japan, the Supreme Commander of the Allied Powers ordered the Imperial General Headquarters abolished on 13 September 1945.
Middle-ranking officers of Army and Navy General Staff, and Army and Navy Ministry, met from time to time at middle-level liaison or study conferences to discuss Japan's strategic war plans, and especially, plans requiring cooperation between the two armed services, outside of the formal meeting in the presence of the Emperor.
Relations between the Japanese Army and Navy were never cordial, and often marked by deep hostility. The Army saw the Soviet Union as Japan's greatest threat and for the most part supported the Hokushin-ron concept that Japan's strategic interests were on the Asian continent. The Navy looked across the Pacific Ocean and saw the United States as the greatest threat, and for the most part supported the Nanshin-ron concept that Japan's strategic interests were in Southeast Asia and the Pacific islands.