He does so by executive without special authority of Congress. This was mostly provoked by Germany's announcement of unrestricted naval attacks.
Citation:
Editors. "Woodrow Wilson orders arming of U.S. merchant ships".
The Literary Encyclopedia. First published 01 March 2010
[http://www.litencyc.com/php/stopics.php?rec=true&UID=12446, accessed 24 May 2013.]