We consider the vaccine allocation problem under scarce supply. We formulate the problem as a two stage stochastic programming model, considering the uncertain factors such as vaccine efficacy, disease spread dynamics and the amount of future supply. We discuss two variants of the model that could be used under different preferences. We demonstrate the usability of our formulations on two case study examples that are generated based on real-life data. The results demonstrate that incorporating the uncertainty in these factors into the decision making process would allow the policy makers to use more effective strategies with an adaptive nature. This is also indicated by the value of stochastic solution, which shows a significant enhancement in disease control gained by the stochastic programming solution compared to a plan based on expected figures.