Similar to FourSquare, social networkers with Facebook's iPhone app can 'check in' to available places as well as tag friends that are with them. The service can also be accessed via the touch.facebook.com mobile site.
However, according to an MoD document, which was seen by The Register, staff could potentially put themselves at risk "by drawing attention to their exact whereabouts".
It also offers step-by-step instructions on how to opt-out of Facebook Places.
"The main concern relating to the use of the application is that it may inadvertently compromise the locality of a military user. Of significant note, users on operations in Northern Ireland," the document reads.
"Social network sites already provide an extensive open source intelligence-gathering tool. This application [Facebook Places] is almost creating a one-stop-shop targeting pack, which could potentially be used to target military personnel, family and friends."
A spokesperson for the MoD said the document was "guidance on how to use social media safely and responsibly" and that "personnel were not instructed to remove the application".
Facebook says its Places service offers "unprecedented" privacy controls.