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The beacon signals from a geostationary satellite were observed using three-element very long baseline interferometry (VLBI), and the phase fluctuations along the baselines between three sites were obtained. The atmospheric phase fluctuations at each observation site were derived from the baseline phase fluctuation data. The fluctuations were classified into three time-interval regions based on the dependence of the Allan standard deviation of the fluctuations on the time interval. In the region where the interval was less than a few seconds and in the one where it was greater than one hundred seconds, the curve of the Allan standard deviation was steep and showed the property of white phase noise. In the region between these two regions, the dependence of the Allan standard deviation on the time interval was weak. The magnitude of the Allan standard deviations for the three observation sites showed time variations in the region where the time interval was longer than a few seconds. Comparison with the weather conditions suggested that the time variations of the Allan standard deviation reflected atmospheric instability above the sites.