The future high energy and nuclear physics experiments will require experiment control systems that operate at a higher level of automation, flexibility, and robustness. In this paper a multi-agent system based framework (AFECS) is presented as an alternative methodology to control large-scale experiments. AFECS creates a control system environment as a collection of software agents behaving as finite state machines. These agents can represent real entities, such as hardware devices, software tasks, or control subsystems. AFECS agents can be distributed over a variety of platforms. Agents communicate with their associated physical components using range of communication protocols, including tcl-DP, cMsg (publish-subscribe communication system developed at Jefferson Lab), SNMP (simple network management protocol), EPICS channel access protocol and JMS.