— Agents are being recommended as a next generation model for revising and restructuring the complex distributed applications. So the task of engineering quality for agent systems has also become significant. As different stakeholders such as project managers, users, and practitioners have different interpretations of quality; an integrated specification of MAS quality that could satisfy all the stakeholders in the project is required. The quality specifications of stakeholders are subjective and, there is a fair chance of non-zero hesitation part in recommending quality specifications; Intuitionistic Fuzzy Sets (IFS) have been used to capture the uncertainties associated with stakeholders’ recommendations. IFS are generalization of fuzzy sets having membership, non-membership and hesitation, and this paper proposes a methodology to obtain prioritization of quality specifications that assists quality engineer in achieving the desired level of quality for Multi-agent systems.