The rise of the fourth industrial revolution and the interest in autonomous production led to increased adoption of Cyber-Physical Production Systems (CPPS) in the industry. Due to the significant suitability of Multi-Agent Systems in building cyber-physical production systems compliant with the Reference Architectural Model Industry 4.0 (RAMI 4.0), more CPPS are being realized using Industrial Agents. Because of their complexity, guidelines for conducting virtual commissioning of agent-based CPPS are required. This paper proposes a novel framework for the virtual commissioning of agent-based CPPS. The framework contributions reside in incorporating both high-level and low-level control verification and validation (V&V) and employing two combined SIL and HIL approaches during the virtual commissioning of agent-based CPPS. The feasibility of the framework was demonstrated during the V&V of an agent-based CPPS on an industrial-scale laboratory robotized production cell. The framework had a significant impact on reducing the cost and efforts of the agent-based CPPS virtual commissioning.