Since networks and computing systems are vital components of today's life, it is of utmost importance to endow them with the capability to survive physical and logical faults, as well as malicious or deliberate attacks. When the information system is obtained by federating pre-existing local systems, a methodology is needed to integrate security policies and mechanisms under a uniform structure. Therefore, in building distributed information systems, a methodology for analysis, design and implementation of security requirements of data and processes is essential for obtaining mutual trust between cooperating organizations. Moreover, when the information system is built as a cooperative set of e-services, security is related to the type of data, to the sensitivity context of the cooperative processes and to the security characteristics of the communication paradigms. The CoopSIS (Cooperative Secure Information Systems) project aims to develop methods and tools for the analysis, design, implementation and evaluation of secure and survivable distributed information systems of cooperative type, in particular with experimentation in the Public Administration Domain. This paper presents the basic issues of a methodology being conceived to build a trusted cooperative environment, where data sensitivity parameters and security requirements of processes are taken into account. The milestones phases of the security development methodology in the context of this project are illustrated.