The following guidelines apply to goverment employees -- both military and civilian -- traveling on official government business.
When traveling to another installation
Use of available government lodging (http://dodlodging.net) is required for all uniformed military personnel and encouraged for civilian personnel. Travelers must provide a justification or certificate of non-availability (CNA) in the remarks section if billeting is not available on a base. Only then are military personnel visiting DOD installations eligible to stay in a commercial hotel.
Commercial lodging availability
For OCONUS travel, it is the traveler's responsibility to make lodging reservations within the Per Diem and (CNA) military requirement. Commercial Lodging is not made in the Defense Travel System (DTS).
For OCONUS, hotel tax and fees are paid as part of the per diem and not claimed separately.
Beware of online booking agents
As of November 2010, the Joint Federal Travel Requirements clearly state that a traveler may not be reimbursed for a hotel booked using online booking agents unless an itemized receipt from the hotel is provided. Most hotels won’t provide an itemized receipt unless you book through them directly. Therefore, you should avoid using online booking agents like Priceline.com, Hotels.com, or Expedia.com, even if they offer better rates.
A traveler must not submit a 'lost receipt' statement to substitute for an online booking hotel receipt.