One of the components necessary to determine the width of a safe maneuvering area on two-way fairways is a safe passing distance. Existing methods do not consider modern model studies of interactions between passing vessels, additionally, they ignore the influence of the vessel’s position accuracy and navigators’ qualifications. This paper presents a method to determine the passing distance, which is free of the drawbacks of the methods used so far. The proposed method is based on simulation research carried out using an FMBS-type (Full Mission Bridge) simulator. The tests were carried out for three loaded vessels (bulk carrier, tanker, and sea ferry), on four sections of the fairway with different parameters and aids-to-navigation available. The results obtained allowed the modification of the authors’ previous, but still widely used, deterministic–probabilistic MTE (Marine Traffic Engineering) method for determining the width of a safe maneuvering area.