In model checking a system design against a set of properties, coverage estimation is frequently used to measure the amount of system behavior being checked by the properties. A popular coverage estimation method is to mutate the system model and check if the mutation can be detected by the given properties. For each mutation and each property, a full model check is required by some state-of-the-art coverage estimation methods. With such repeated model checking, mutation-based coverage estimation becomes significantly time-consuming. To alleviate this problem, a partial model checking (PMC) technique is proposed to recheck only those system states that were affected by a mutation, thus unnecessary rechecking of a large portion of the system states is avoided and time is saved. The PMC method has been integrated into the State Graph Manipulators model checker. Applying the proposed method to several examples showed that PMC has a saving of 50% to 70% in the coverage estimation time, and a reduction of 90% in mode visits.