After the outbreak of the Civil War,
Georgia Governor Joseph E. Brown appointed Harrison a brigadier general of state troops to rank from September 14, 1861. Harrison was assigned to establish a training camp near Savannah and to organize the regiments for the new troops. Harrison did this, and led a force guarding the Georgia coast, during the winter of 1861–1862, after which his command was terminated. Under a new militia law in 1864, Harrison was appointed colonel in charge of Georgia's First Military District with the duties of destroying
whiskey stills and tracking down
deserters. Soon, Harrison's command was required to oppose
Sherman's March to the Sea. When they reached the Savannah area, Sherman's men pillaged Harrison's home and property at Montieth. In December 1864, Harrison was taken prisoner while visiting his devastated property. Harrison was released from prison before the end of the war but refused to take the oath of allegiance to the
United States government. ==Later life==