There are limited studies on the use of ship domain as the safety criterion for ship navigation within confined waters. In this paper, a free-form ship domain has been developed empirically for navigation in confined waters. Two individual domains of an asymmetrical polygonal shape have been assumed around the own ship and target ship, and the size of the ship domains is assumed to be dynamically enlarged with increased ship speeds. The required safe distance modelled using the proposed ship domain takes into account dynamic changes in relative bearing and heading. The model is calibrated using the data of vessel movements in Singapore Strait and Singapore Port. An innovative process has been adopted that iteratively adjusts the parameters in the basic ship domain of a stationary ship; a speed function as well as a weight function to maximise the usage of the dataset. The resulting ship domain model compares well with existing ship domains for typical encounters, such as those of Fujii and Coldwell but represents non-typical encounters more effectively than existing models.