The Division of Military and Naval Affairs administers the State's military forces and facilities and coordinates the State's emergency preparedness plans and response to disasters. The military forces consist of the New York Army National Guard, the New York Air National Guard, and the New York Naval Militia, which serve as reserve components to the United States Army, Air Force, and Navy. They can be activated by the Federal government or the governor in times of emergency. The New York Guard is organized to provide a State reserve force if the Army National Guard is ordered into Federal service. The division also administers the State Reserve and Retired Lists of military personnel. The division includes the State Emergency Management Office, which adopts and promulgates statewide disaster plans. 

The first State constitution of 1777 and all subsequent constitutions designated the governor as commander-in-chief of the State's armed forces. In 1786 the governor appointed an adjutant general to supervise the militia and all military establishments in the State. The governor was authorized to appoint an adjutant general by the constitutions of 1821 and 1846 in response to the passage of a federal statute of 1792 requiring each state to appoint such an officer. During the nineteenth century various staff officers, including inspector general, commissary general, judge advocate, quartermaster general, surgeon general, paymaster general, and engineer-in-chief, were established by statute or by the constitution to assist the adjutant general. In 1862 (Chapter 477) the organized militia was officially designated as the National Guard of New York State. The State Naval Militia was established by law in 1889 (Chapter 492).

The 1894 constitution authorized the governor to appoint a military secretary in addition to the adjutant general. From 1894 until 1926 the military secretary and the adjutant general shared responsibility for supervising the State's defense. A consolidated military law enacted in 1909 (Chapter 41) provided that the adjutant general assume the duties of all existing staff offices.

In 1926 (Chapter 546), a year after ratification of the constitutional reorganization of State government, the Division of Military and Naval Affairs, headed by an adjutant general appointed by the governor, was established within the Executive Department. In addition to assuming responsibility for the State's military and naval staff departments, the Division took over supervision of the State Soldiers' and Sailors' Home at Bath (renamed the State Camp for Veterans), the New York State Monuments Commission for the Battlefields of Gettysburg, Chattanooga, and Antietam, the Bureau for the Relief of Sick and Disabled Veterans, and the New York State Bonus Commission.

The Bath facility was incorporated in 1876 (Chapter 270) as the Grand Army of the Republic Soldiers' Home of the State of New York under the direction of a board of trustees to house honorably discharged veterans of the Civil War. Two years later (Chapter 48) it was taken over by the State and renamed the New York State Soldiers' and Sailors' Home. The Monuments Commission, consisting of three veterans appointed by the Adjutant General, was created in 1913 (Chapter 550) to continue the work of erecting memorials to New York State's participation in the Civil War battles at Gettysburg, Chattanooga, and Antietam. Several earlier commissions were charged with memorializing these battlefields individually. The New York Veterans Relief Commission, consisting of the adjutant general, comptroller, and attorney general, was established in 1922 (Chapter 589) to administer State financial aid to disabled World War I veterans. The following year (Chapter 326) the commission was replaced by the Bureau for the Relief of Sick and Disabled Veterans under the adjutant general. The Bonus Commission, consisting of the adjutant general, comptroller, attorney general, and treasurer, was established in 1924 (Chapter 19) following a 1923 constitutional amendment allowing the State to provide direct bonus payments to honorably discharged veterans of
World War I. 

When the Division of Veterans Affairs was created in 1945 (Chapter 763) to provide services to returning World War II veterans, the adjutant general was designated chairman of its Veterans Affairs Commission, an advisory body. In 1949 (Chapter 498) the adjutant general was replaced with the newly created position of chief of staff to the governor as head of the Division of Military and Naval Affairs. The State Civil Defense Commission was established in 1951 (Chapter 784) as an independent unit in the Executive Department to prepare for the State's defense in the event of attack. The commission was transferred to the Department of Transportation in 1971 (Chapter 73), and some of its functions were dispersed to other agencies. In 1973 (Chapter 93) the commission was transferred to Division of Military and Naval Affairs, with its former functions reinstated and with the additional responsibility for coordinating statewide disaster planning. More recently it was renamed the State Emergency Management Office (SEMO).