We investigate the problem of locating the source of diffusion in complex networks without complete knowledge of nodes' states. Some currently known methods assume the information travels via a single, shortest path, which by assumption is the fastest way. We show that such a method leads to the overestimation of propagation time for synthetic and real networks, where multiple shortest paths as well as longer paths between vertices exist. We propose a new method of source estimation based on maximum likelihood principle, that takes into account existence multiple shortest paths. It shows up to 1.6 times higher accuracy in synthetic and real networks.