The following documents were discovered by The Black Vault that pertain to reporting UFOs by the U.S. Military, Government and Commercial installations.
Air Force Instruction 10-206. 2008 Revision with UFO references [87 Pages] - Up until 2011, the Air Force had this publication active, and UFOs remained in it to be reported. When The Huffington Post profiled The Black Vault, and this discovery, the publication was changed within days. Reference: Air Force UFO Rules Vanish After Huffington Post Inquiry. Air Force Instruction 10-206. 2011 Revision without UFO references [40 Pages, 0.4MB]
Air Force Regulation 200-2 [8 Pages, 4.76mb] - This Regulation establishes procedures for information and evidence material pertaining to unidentified flying objects and sets forth the responsibility of Air Force activities in this regard. It applies to all Air Force Activities.
DoD 5040.6-M-1, October 21, 2002, Decision Logic Table Instructions for Recording and Handling Visual Information Material [64 Pages, 0.3 MB] - In this DOD manual, dated 2002 and is still on the books, references what military personnel should do given they take a photograph of a UFO.