Developers are struggling with the challenging task of producing secure e-commerce software. Nonetheless, software insecurity remains an issue for e-commerce organisations. Software engineers are expected to possess knowledge in the software engineering area, as well as, security. In addition, they are required to understand and correctly identify the relationships between the security concepts. However, developers commonly lack this knowledge and consequently, security is often omitted during the engineering process. To support developers to face the challenge, we use ontology based techniques for structuring and representation of security knowledge. Categorization according to the security properties of confidentiality, integrity, and availability is needed to provide a holistic view over the security requirements, assets, security threats, and security controls. Moreover, we propose mapping of different security ontologies to provide traceability. For this purpose, we use meta-agents and software agents in multi-agent system. We present a development scenario of electronic invoice presentment system, where we demonstrate how usage of ontologies in combination with multi-agent system can improve security of e-commerce software systems.