A network system, a node apparatus, a control apparatus, a communication control method, and a control method are provided that make it possible to easily perform control of a physical layer device required for flow control. In a communication system including a plurality of nodes constituting a network and a control apparatus controlling each node in units of flows, at least one communication interface is provided to each port of the nodes; the control apparatus instructs the node to set a physical layer mode on a port, and the node, in accordance with the physical layer mode indicated by the control apparatus, make setting of a corresponding communication interface.