Tracking devices small enough to be implanted would have to be RFID devices. The problem with that is that the RFID has to pass within a few feet (less than 10) of a detector to work. Also, if I were in the military, there is no way in hell I would allow them to inject a tracking device under their skin.
That is why I said "future". They are working the technology. I am in the military, and if the order came down for me to implant this device under my skin, I don't know what I would do. I would weigh out the options I guess. If I refused to obey the order they may discharge me which effects more than me, it effects first my wife and kid, and depending on the status of war, it could effect others as well. I would consider it, but it would weigh heavy.