Over the administration of justice the military authorities exercised a close supervision. Instructions were sent out to court officers covering the selection of juries, the suspension of certain laws, and the rules of evidence and procedure. Courts were often closed, court decrees set aside or modified, prisoners released, and many cases reserved for trial by military commission. Some commanders required juries to admit Negro members and insisted that all jurors take the "ironclad" test oath. There was some attempt at regulating the Federal courts but without much success.

Since the state legislatures were forbidden to meet, much legislation was enacted through military orders. Stay laws were enacted, the color line was abolished, new criminal regulations were promulgated, and the police power was invoked in some instances to justify sweeping measures, such as the prohibition of whisky manufacture in North Carolina and South Carolina. The military governors levied, increased, or decreased taxes and made appropriations which the state treasurers were forced to pay, but they restrained the radical conventions, all of which wished to spend much money. According to the Act of March 23, 1867, the generals and their appointees were to be paid by the United States, but in practice the running expenses of reconstruction were paid by the state treasurers.