Virtual Reality (VR) simulators can offer alternatives for training procedures in the medical field. Most current VR simulators consider single-node contact for interacting with an object to convey displacement and force on a discrete mesh. However, a single-node contact does not closely simulate palpation, which requires a surface made of a multi-node contact to touch a soft object. Thus, we hypothesize that the softness of a deformable object (such as a virtual breast phantom) palpated through a single-node contact would be perceived differently from that of the same phantom palpated through a multi-node contact with various force arrays. We conducted a study to investigate this hypothesis. Using a co-located VR setup that aligns visual and haptic stimuli onto a spatial location, we tested 15 human participants under conditions of both visual and haptic stimuli available and only visual (or haptic) stimulus available. In a trial, each participant palpated and discriminated two virtual breast phantoms of same softness through different contacts with varying force arrays. The results of this study revealed that virtual breast phantoms palpated through a single-node contact were constantly perceived harder than their counterparts palpated through a multi-node contact with varying force arrays, when visual stimuli were available. These results imply a constraint for developing a VR system of training palpation.