Federated cloud systems increase the reliability and reduce the cost of the computational support. The resulting combination of secure private clouds and less secure public clouds, together with the fact that resources need to be located within different clouds, strongly affects the information flow security of the entire system. In this paper, the clouds as well as entities of a federated cloud system are assigned security levels, and a probabilistic flow sensitive security model for a federated cloud system is proposed. Then the notion of opacity—a notion capturing the security of information flow—of a cloud computing systems is introduced, and different variants of quantitative analysis of opacity are presented. As a result, one can track the information flow in a cloud system, and analyze the impact of different resource allocation strategies by quantifying the corresponding opacity characteristics.