The rule of the five generals lasted in all the States until June 1868, and continued in Mississippi, Texas, Virginia, and Georgia until 1870. There had been, to be sure, some military government in 1865, subject, however, to the President, and from 1865 to 1867 the army, along with the Freedmen's Bureau, had exerted a strong influence in the government of the South, but in the regime now inaugurated the military was supreme. The generals had a superior at Washington, but whether it was the President, General Grant, or Congress was not clear until the Act of July 19, 1867 made Congress the source of authority.

The power of the generals most strikingly appeared in their control of the state governments which were continued as provisional organizations. Since no elections were permitted, all appointments and removals were made from military headquarters, which soon became political beehives, centers of wirepulling and agencies for the distribution of spoils. At the outset civil officers were ordered to retain their offices during good behavior, subject to military control. But no local official was permitted to use his influence ever so slightly against reconstruction. Since most of them did not favor the policy of Congress, thousands were removed as "obstacles to reconstruction." The Governors of Georgia, Louisiana, Virginia, Mississippi, and Texas were displaced and others appointed in their stead. All kinds of subordinate offices rapidly became vacant. New appointments were nearly always carpetbaggers and native radicals who could take the "ironclad" oath. The generals complained that there were not enough competent native "loyalists" to fill the offices, and frequently an army officer was installed as governor, treasurer, secretary of state, auditor, or mayor. In nearly all towns, the police force was reorganized, and former Federal soldiers were added to the force, while the regular troops were used for general police purposes and for rural constabulary.