In the first years of the 19th century, Fox was responsible for fitting out some of the gunboats that were the Republican Jefferson Administration's unsuccessful attempt at creating a "Naval Militia." In 1804, secretary of the Navy, Robert Smith sent for Fox to come to Washington, D.C. and convinced him to become the naval constructor at the Washington Navy Yard. Smith endorsed Fox as " a scientific as well as a practical man, stands high among the first in his profession." At that navy yard Fox was to superintend the construction and repair of naval vessels. Thomas Tingey had overall charge of the yard and its employees, however, as naval constructor, Fox reported to the secretary of the Navy and directed the largest and most skilled group of mechanics and laborers. Fox's salary as constructor for the WNY was increased to a generous $2000.00 per annum with $500.00 additional allowance for housing, and the liberty of taking as many apprentices as he chose. During these years, Fox designed the sloop of war and oversaw major repairs to the frigates , "President" and "Essex". Despite the navy yard's progress in building and repairing vessels, Fox's relationship with Commodore Tingey deteriorated over time. Tingey believed in discipline, and deference to authority and was a firm believer in the chain of command. Fox on the other hand considered his appointment by the secretary of the Navy sufficient to ignore yard policy when it suited. By 1806 each man was complaining to the secretary about the other. While the two had differing personalities a substantial part of their dilemma was the confusing reporting relationships. Tingey had overall charge of the shipyard but Fox was hired by and reported directly to the secretary of the Navy. One proof of the structural nature of this problem is that William Doughty Fox's successor, experienced similar difficulties in his dealing with both Tingey and the subsequent Commandant Isaac Hull.