SUMMARY Monitoring seismic velocity changes obtained from ambient noise correlations is widely used to understand changes in rock properties in response to earthquakes, volcanic activities and environmental changes. Since continuous seismic data have been accumulated, this method can estimate long-term changes in seismic velocity, such as crustal recovery after a major earthquake and temporal variations in seismic velocity related to long-term environmental change. Changes in seismic velocity can be estimated with a high temporal resolution by measuring the phase differences of ambient noise correlations based on a seismic interferometry method. Still, these phase differences are influenced not only by seismic wave velocity changes but also by errors in clock timing in seismometers. The clock drift occurs due to out-of-synchronization with the GPS clock and the drift of the internal clock. Therefore, to accurately monitor temporal changes in crustal structure by measuring the phase differences of noise correlations, it is crucial to evaluate the contribution of errors in clock timing to the phase differences. Recently, a method using an extended Kalman filter based on a state-space model was developed for reliable detection of temporal changes in the waveforms of ambient noise correlations, with the state-space model offering the advantage of flexible modelling of time-series data. In this study, we incorporated the time-shifts caused by clock time errors of the seismometer into the state-space model of the temporal changes in ambient noise correlations. We estimated seismic velocity changes, amplitude changes of noise correlations and clock time errors from 2010 April to 2021 September at seismic stations around the Shinmoe-dake volcano in Japan, which experienced eruptions in 2011 and 2018, respectively. Several stations exhibited clear clock time offsets, and the occurrence of clock time-shifts coincided with the dates when the data logger was turned off for seismic station maintenance or replacement of the seismometer. The proposed method provides stable estimations with respect to the signal-to-noise ratio of the waveform, and this stable estimation facilitates accurate timing of seismic recordings, enabling precise analysis of seismic phase arrival times.