A few sample citations:
Chicago: U.S. Federal Energy Regulatory Commission. 1977/78. Annual report of the U.S. Federal Energy Regulatory Commission. Washington, D.C.: GPO.
APA: Federal Aviation Administration (2004). Seaplane, skiplane, and float/ski equipped helicopter operations handbook (FAA-H-8083-23). Washington, DC: Government Printing Office.
MLA: United States. Dept of Labor. Employment and Training Administration. Dictionary of Occupational Titles. 4th ed. Washington: GPO, 1977. Print.
Many times a government agency will be listed as the author, unless there is an individual personal author.
Since many government documents are online, you will often be following the citation guidelines for electronic resources just as you would for other online articles, web pages, etc.
Depending on the level of the agency and citation style, it may be listed as a sub-agency (as in the MLA example above). Note also the placement of the date and formatting of publication location change based on the citation style.