Human visual system extracts or creates various rich information from low-level visual features. Animacy perception, where an obviously non-animate object elicits to us a feeling that the object is animate, is also susceptible to motion trajectory. For example, a simple dot, when moving with the random trajectory based on 1/f fluctuation, provide a vivid sensation of animacy. Recently, we found that perceived animacy from a randomly moving dot was drastically decreased by the presence of other dots that made synchronous motion with the target dot. However, in our previous study, the synchronous motion accompanied the spatial alignment, and hence it is unclear whether the synchronous motion per se or the spatial alignment is responsible for the modulation of animacy perception. The present study investigated the effects of these two factors by manipulating the spatial alignment independently from the motion synchrony. Consequently, we found that the reduction of perceived animacy from both spatially aligned as well as spatially misaligned synchronous motion, wherein the magnitudes of animacy reduction were quantitatively comparable. These results suggested that the synchronous motion is primal factor to reduce the perceived animacy, whereas the effect of spatial alignment was negligible.