Morse's work as Pacific Coast Arbitrator and on other presidential labor commissions brought him nation-wide repute in the pre-war years. After America's entry into World War II it became crucial to manage labor disputes with as little confrontation as possible. To arbitrate and settle disputes before they could damage the war effort the Roosevelt administration created the National War Labor Board (NWLB). The twelve-member panel was composed of four representatives of business, four labor men, and four "neutral" members who were to act in the best interests of the public. In January of 1942 President Roosevelt called Morse to Washington where he quickly adopted a leadership position on the board.

Charged with maintaining labor peace, the NWLB mostly worked on the resolution of wage disputes. Shortly after Roosevelt's war announcement, both the CIO and the AFL made a patriotic No-Strike Pledge for the duration of the war, abandoning their most potent weapon and essentially throwing themselves on the mercy of the NWLB. For the most part, the public members of the board were sympathetic to labor's plight, but rapid inflation in 1942 necessitated that they keep wage raises to a minimum.

In an effort to keep wages in line, the NWLB came up with a policy known as the Little Steel Formula. First applied to the steel industry then to a wide range of occupations, the formula allowed wage increases only at levels that would not increase inflation. Unionists argued that Little Steel fundamentally crippled collective bargaining and that wage increases were constantly behind inflation, keeping workers poor while corporations raked in incredible profits.

Recognizing that the No-Strike Pledge and wage controls caused a double burden for unionists, the board, following Morse's lead, established "maintenance of membership" clauses in many of the contracts it arbitrated. Maintenance of membership stipulated that every worker hired by a shop with a union contract would automatically become a member of that union. Moreover, the employer was required to dismiss any employee who did not pay his or her dues and maintain good standing in the union. Although the clause had some negatives for unions, it kept non-union workers from flooding war plants and destroying the gains of the 1930s.

Morse was also instrumental in the National War Labor Board's policy of mandating that women and minority workers receive equal pay for equal work. Although this policy gained only spotty enforcement, the idea prevailed in many other government agencies and governmental guidelines.