Starfleet vessels can synchronize their internal chronometers with a Federation time beacon. This was mostly done when the Captain, or other bridge officers for that matter, suspected the starship's chronometers were not displaying the correct time.
The USS Enterprise-D used a time beacon after they managed to break free of a causality loop, to determine the amount of time they had spent inside it. It turned out the Enterprise was inside the loop for 17.4 days. (TNG: "Cause and Effect")
It is unknown what a time beacon looked like and where they where placed. Given the fact that the Federation used subspace relay stations and starbases deployed around the galaxy, within their sphere of influence, it seems plausible that time beacons were incorporated into such structures. To create separate devices which would float in space or be based on remote planets seems inefficient.