In a method for estimating a noise level representing the magnitude of a noise component from measurement data, first waveform data composed of high frequency noise components extracted from assumed noise data are divided into segments so that each section where positive values successively occur or each section where negative values successively occur in the first waveform data is defined as one segment. A segment-width threshold is determined based on the distribution of the widths of the segments. Second waveform data composed of high frequency noise components extracted from measurement data are divided into segments in the same manner. Each segment having a width larger than the threshold is excluded from the segments in the second waveform data, to create a first segment group. The noise level is determined based on the heights or areas of the plurality of segments included in the first segment group.