Diffusion processes in networks are increasingly used to model dynamic phenomena such as the spread of information, wildlife, or social influence. Our work addresses the problem of learning the underlying parameters that govern such a diffusion process by observing the time at which nodes become active. A key advantage of our approach is that, unlike previous work, it can tolerate missing observations for some nodes in the diffusion process. Having incomplete observations is characteristic of offline networks used to model the spread of wildlife. We develop an EM algorithm to address parameter learning in such settings. Since both the E and M steps are computationally challenging, we employ a number of optimization methods such as nonlinear and difference-of-convex programming to address these challenges. Evaluation of the approach on the Red-cockaded Woodpecker conservation problem shows that it is highly robust and accurately learns parameters in various settings, even with more than 80 % missing data.