I assume that the agency that you are talking about is the United States Railroad Administration. This was an agency set up during World War I to try to ensure that the railroads (the major method of transportation at that time) would run smoothly.
At the beginning of WWI, both the railroad companies and the railroad unions were doing things that made it hard for the railroads to operate efficiently. The companies wanted to continue to make lots of money and the unions wanted to force higher wages. Even when railroads cooperated, there was the problem of antitrust legislation that made it so that such actions were possibly illegal.
To get around all of these problems, Pres. Wilson simply nationalized the railroads. From that point on, the government ran the railroads. It did so in order to make sure that men and materiel would be able to make it to ports in order to be shipped off to Europe.