The evacuation of the population from flood-affected regions is a non-structural measure to mitigate flood hazards. Shelters used for this purpose usually accommodate a large number of flood evacuees for a temporary period. Floods during a pandemic result in a compound hazard. Evacuations under such situations are difficult to plan as social distancing is nearly impossible in the highly crowded shelters. This results in a multi-objective problem with conflicting objectives of maximizing the number of evacuees from flood-prone regions and minimizing the number of infections at the end of the shelter's stay. To the best of our knowledge, such a problem is yet to be explored in literature. Here we develop a simulation-optimization framework, where multiple objectives are handled with a max-min approach. The simulation model consists of an extended Susceptible-Exposed-Infectious-Recovered-Susceptible model. We apply the proposed model to the flood-prone Jagatsinghpur district in the state of Odisha, India. We find that the proposed approach can provide an estimate of people required to be evacuated from individual flood-prone villages to reduce flood hazards during the pandemic. At the same time, this does not result in an uncontrolled number of new infections. The proposed approach can generalize to different regions and can provide a framework to stakeholders to manage conflicting objectives in disaster management planning and to handle compound hazards.