With the outbreak of the Second World War in September 1939, the Chiefs of Staff (COS) Committee became a permanent committee reporting to the War Cabinet. Major-General Ismay, hitherto Secretary of the Committee on Imperial Defence, was appointed Deputy Secretary on the military side of the War Cabinet, and also Secretary to the COS Committee. The official business of the COS in their corporate capacity was to hear reports and consider the situation, to decide day to day problems concerning operations, and to consider any matters specially remitted to them by the War Cabinet. They were in fact the joint advisers of the War Cabinet on military policy. Moreover, by having frequent meetings and an efficient organisation they became in time an executive body which issued instructions in its corporate capacity to commanders in the field.
The COS Committee was served by two inter-service bodies: the Joint Planning Staff and the Joint Intelligence Sub-committee. As the war developed, the increasing pressure on the time and energy of the COS Committee prompted the government to appoint (on 22 April 1940) three Vice-Chiefs of Staff, who acted as substitutes for their own Chiefs, and whose meetings counted equally as meetings (the Vice-Chiefs of Staff Committee) of the COS Committee.
On the formation of the National Coalition Government on 11 May 1940, the Prime Minister, Winston Churchill, said that a 'key change' he had made was the supervision and direction of the COS Committee by a Minister of Defence with undefined powers, who was also Prime Minister. The Chief Staff Officer to the Minster of Defence became an additional member of the COS Committee (Major-General Ismay being appointed to the post).
Meetings were sometimes attended by representatives of the Dominions, by officials of the Foreign Office or the Ministry of Economic Warfare, by commanders-in-chief when they were in London, and by the Chief of Combined Operations when matters affecting overall strategy were under discussion. The Committee was chaired by Sir Cyril Newall (Chief of the Air Staff) to October 1940; Sir Dudley Pound (Admiral of the Fleet) to March 1942; and Sir Alan Brooke (Chief of the Imperial General Staff) for the remainder of the war. On occasions, Churchill presided, in which case meetings were known as staff conferences. As the war proceeded, Churchill tended to work directly through the COS Committee rather than through the War Cabinet.
In December 1946, most of the work of the former military section of the War Cabinet Office, including the COS Committee, was transferred to the Ministry of Defence.