In the early part of the war he served as a staff officer of Brig. Gen. Joseph K. Mansfield in Washington, D.C., and then he commanded the defenses of Fernandina, Florida. In the fall of 1862, Dutton began to form and train the volunteer 21st Connecticut Infantry Regiment in Norwalk. On September 5 he was commissioned the unit's colonel and commanding officer. The 21st Connecticut was organized as part of the IX Corps, Army of the Potomac. He then brought his regiment to Washington on September 11, and by November they were posted to Arlington Heights in Virginia as part of the defenses of Washington. From November 7–19 Dutton and his regiment marched to Falmouth, Virginia, and that December they fought during the Battle of Fredericksburg.