An estimate of the on-site wave spectrum can be obtained from measured ship responses by use of Bayesian modelling, which means that the wave spectrum is found as the optimum solution from a probabilistic viewpoint. The paper describes the introduction of two hyperparameters into Bayesian modelling so that the prior information included in the modelling is based on two constraints: the wave spectrum must be smooth directional-wise as well as frequency-wise. Traditionally, only one hyperparameter has been used to control the amount of smoothing applied in both the frequency and directional ranges. From numerical simulations of stochastic response measurements, it is shown that the optimal hyperparameters, determined by use of ABIC (a Bayesian Information Criterion), correspond to the best estimate of the wave spectrum, which is not always the case when only one hyperparameter is included in the Bayesian modelling. The paper includes also an analysis of full-scale motion measurements where wave spectra estimated by the Bayesian modelling are compared with results from ocean surface measurements by satellite and from a wave radar. The agreement is found to be reasonable.