On July 31, 1989, President George H. W. Bush nominated Howard as Under Secretary of the Navy. After confirmation by the United States Senate, Howard entered office on August 7, 1989. Howard's time as Under Secretary was dominated by the collapse of the Soviet Union and the subsequent catastrophic drop in the defense budget, the 1991 Gulf War and the post-war Tailhook scandal.
He took over as Acting Secretary of the Navy in June, 1992 when Secretary of the Navy Henry L. Garrett III was forced to resign by President Bush in the wake of that scandal. Howard immediately ordered a Navy and Marine Corps-wide "standdown" for training designed to prevent sexual harassment. Defense Comptroller Sean O'Keefe replaced him as Acting Secretary the following month. The Department of Defense Inspector General issued a blistering report in September 1992 in which he concluded that Under Secretary Howard, the Naval Inspector General, the Judge Advocate General and the Director of Naval Investigative Service (NIS) had failed to conduct an adequate investigation into allegations of misconduct; had been overly focused on lower ranking personnel; and had been more concerned with protecting the reputation of the United States Navy than with getting to the bottom of the allegations.[1] It was widely speculated that O'Keefe would have Howard (and the Navy IG) resign at the same time that Judge Advocate General Rear AdmiralJohn E. Gordon and NIS Director Rear Admiral Duvall M. Williams, Jr. were ousted for their attempts to turn the Tailhook investigation into a whitewash, but, in a move that drew surprise, O'Keefe announced that he continued to have "complete confidence" in Under Secretary Howard saying that he was much more "sinned against than sinned."[1] As such, Howard served out the rest of the Bush administration and left office on January 20, 1993. Howard retired from the Foreign Service in June, 1993 with the rank of Minister-Counselor and received the Meritorious Honor Award for career achievements.