Overview
During the Civil War a number of secret operations sprang up, some at the direction of the government, some with its tacit approval, and some that were under only the most tenuous control, or even under no control whatsoever. Many of these operations involved acts that were considered, by the Union, to go beyond the normal conduct of "civilized" warfare. From the Confederacy's point of view, these were desperate measures necessary to compensate for the fact that, in terms of conventional warfare, they were out-manned, out-supplied, and out-gunned. By 1864, the Confederate government was attempting to gain control over the various operations that had sprung up since the beginning of the War, but often with little success. In April 1865, most of the official papers of the Secret Service were burned by Confederate Secretary of State Judah P. Benjamin just before the Confederate government evacuated Richmond, so the full story of Confederate secret operations may never be known.
In 1864, secret legislation was put before the Confederate Congress to create an official Special and Secret Bureau of the War Department. The legislation was not enacted until March 1865 and was never implemented, so no one really knows what an official "Confederate Secret Service" would have looked like. However, all these various bits and pieces have been referred to at one time or another as having been part of the Confederate Secret Service.
Read more about this topic: Confederate Secret Service