The leakage of secret information via a public channel is a critical privacy flaw in software systems. The more information is leaked per observation, the less time an attacker needs to learn the secret. Due to the size and complexity of the modern software, and because some empirical facts are not available for a formal analysis of the source code, researchers started investigating statistical methods using program executions as samples. However, current statistical methods require a high sample coverage. Ideally, the sample is large enough to contain every possible combination of secret$\times$observable value to accurately reflect the joint distribution of (secret, observable). Otherwise, the information leakage is severely underestimated, which is problematic as it can lead to overconfidence in the security of an otherwise vulnerable program. In this paper, we introduce an improved estimator for information leakage and propose to use methods from applied statistics to improve our estimate of the joint distribution when sample coverage is low. The key idea is to reconstruct the joint distribution by casting our problem as a multinomial estimation problem in the absence of samples for all classes. We suggest two approaches and demonstrate the effectiveness of each approach on a set of benchmark subjects. We also propose novel refinement heuristics, which help to adjust the joint distribution and gain better estimation accuracy. Compared to existing statistical methods for information leakage estimation, our method can safely overestimate the mutual information and provide a more accurate estimate from a limited number of program executions.