Described embodiments classify packets received by a network processor. A processing module of the network processor generates tasks corresponding to each received packet. A packet classification processor determines, independent of a flow identifier of the received task, control data corresponding to each task. A multi-thread instruction engine processes threads of instructions corresponding to received tasks, each task corresponding to a packet flow of the network processor and maintains a thread status table and a sequence counter for each flow. Active threads are tracked by the thread status table, and each status entry includes a sequence value and a flow value identifying the flow. Each sequence counter generates a sequence value for each thread by incrementing the sequence counter each time processing of a thread for the associated flow is started, and decrementing the sequence counter each time a thread for the associated flow is completed.