A method is disclosed for controlling the flow of packets aggregated from multiple logical ports over a transport link. A directed flow control indicator is provided to the transmitting end station that causes a detected congestion condition. The directed flow control indicator causes the transmitting end station to suspend the transmission of further packets. The linear expansion header of the Generic Framing Procedure (GFP) linear mapping scheme is extended to include the flow control indicator, such as a bit indicating a potential overload condition. A directed flow control indication can be provided in one or more packets sent to the transmitting end station over the transport network without increasing the network overhead. If packets are not being sent to the appropriate transmitting end station, a packet generator can generate one or more packets with the flow control indicator to inform the appropriate transmitting end station of the congestion condition.