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Conflict detection and resolution is a critical capacity for realizing free flight. In this paper, a multi-agent system algorithm is proposed to solve the air traffic conflict detection and resolution problem involving multiple aircraft, where each aircraft may be regarded as an intelligent agent. The conflict detection and resolution problem for each agent is solved as a constraint satisfaction problem. A pair wise, argument-based negotiation approach is established for the aircraft to search for a multilaterally acceptable conflict resolution. The proposed algorithm guarantees to lead to an appropriate solution, except for some extreme cases. It also considers real-time constraints such as response time, negotiation deadline, etc. The ground based air traffic controller is always included in this system, and acts as a high-level supervisor and coordinator. It has authority to approve or override any proposal from any aircraft; force an aircraft to accept a proposal; and open or close a negotiation. It may also join the collaboration to represent those aircraft which lack the capacity to negotiate for themselves. However, in such cases it must obey the same negotiation protocol as other aircraft.