Scanning devices acquire geometric information from the surface of an object in the form of a 3D point set. Such point sets, as any data obtained by means of physical measurement, contain some noise. To create an accurate model of the scanned object, this noise should be resolved before or during the process of surface reconstruction. In this paper, we develop a statistical technique to estimate the noise in a scanned point set. The noise is represented as normal distributions with zero mean and their variances determine the amount of the noise. These distributions are estimated with a variational Bayesian method, which is known to provide more robust estimations than point estimate methods, such as maximum likelihood and maximum a posteriori. Validation experiments and further tests with real scan data show that the proposed technique can accurately estimate the noise in a 3D point set.