Due to the advancements in manufacturing system technology and the ever-increasing demand for personalized products, there is a growing desire to improve the flexibility of manufacturing systems. Multi-agent control is one strategy that has been proposed to address this challenge. The multi-agent control strategy relies on the decision making and cooperation of a number of intelligent software agents to control and coordinate various components on the shop floor. One of the most important agents for this control strategy is the product agent, which is the decision maker for a single part in the manufacturing system. To improve the flexibility and adaptability of the product agent and its control strategy, this work proposes a direct and active cooperation framework for the product agent. The directly and actively cooperating product agent can identify and actively negotiate scheduling constraints with other agents in the system. A new modeling formalism, based on priced timed automata, and an optimization-based decision making strategy are proposed as part of the framework. Two simulation case studies showcase how direct and active cooperation can be used to improve the flexibility and performance of manufacturing systems.