The modern information systems evaluate very quickly. The information is more and more distributed through the networks or federation of numerous information systems located in different places on the globe. Also, the control domain of information system is very important in the times of very fast networks, telecommunication protocols and telecommunication equipment. The paper presents the proposal of cooperation between the information systems and multi-agent systems. It is necessary to assure the cooperation of local data resources and create the coherent structure for intelligent agents. The dynamic process of conflict solving can be realized by using different techniques that come from the multi-agent systems.