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A chronometer was a device used to keep track of time. Starships measure the passage of time when they traverse the space-time continuum other than Albert Einstein's proper time by use of chronometers. (TOS: "The Naked Time", "Tomorrow is Yesterday", "The Mark of Gideon")
Chronometer function could be disrupted by many things, such as the non-application of natural laws of the universe, causing stoppage (TAS: "The Magicks of Megas-Tu") or the reversal of time, causing them to run backward (TAS: "The Counter-Clock Incident").
On occasion, starships may need to reset the ship's clock, i.e., on-board chronometer, at which time a Federation time beacon or a realignment subspace signal by a starbase may be consulted. (TNG: "Clues", "Cause and Effect")