An important problem of reconstruction of diffusion network and transmission probabilities from the data has attracted a considerable attention in the past several years. A number of recent papers introduced efficient algorithms for the estimation of spreading parameters, based on the maximization of the likelihood of observed cascades, assuming that the full information for all the nodes in the network is available. In this work, we focus on a more realistic and restricted scenario, in which only a partial information on the cascades is available: either the set of activation times for a limited number of nodes, or the states of nodes for a subset of observation times. To tackle this problem, we first introduce a framework based on the maximization of the likelihood of the incomplete diffusion trace. However, we argue that the computation of this incomplete likelihood is a computationally hard problem, and show that a fast and robust reconstruction of transmission probabilities in sparse networks can be achieved with a new algorithm based on recently introduced dynamic message-passing equations for the spreading processes. The suggested approach can be easily generalized to a large class of discrete and continuous dynamic models, as well as to the cases of dynamically-changing networks and noisy information.