A master clock generation unit for satellite navigation systems, comprises a plurality of frequency inputs for receiving a respective atomic clock signal, each having a first or a second reference frequency, and a number of frequency converters each having an input connected to one of the frequency inputs and an output. Each of the frequency converters receives an offset frequency (selected according to the first and second reference frequency at the assigned frequency input) from at least one frequency synthesizer, for providing the same intermediate frequency at each of the converter outputs. A switching matrix is connected to each of the converter outputs for selecting one of the intermediate frequencies as a primary clock provided at a first matrix output, and another of the intermediate frequencies as a secondary clock provided at a second matrix output. A frequency generator having an input connected to the first matrix output and connected to a number of frequency outputs of the master clock generation unit, derives an output reference frequency from the primary clock, and provides it at the frequency outputs. A phase meter having a first meter input connected to the first matrix output and a second meter input connected to the second matrix output, determines a phase difference between the primary and the secondary clock for detecting abnormal behavior.