In a network system for transporting GFP-encapsulated Fibre Channel/FICON data across a SONET/SDH transport network between two Fibre Channel/FICON ports, a transport interface for one Fibre Channel/FICON port intelligently allocates the amount of buffers for receiving Fibre Channel/FICON data from the other Fibre Channel/FICON port by determining the latency of travel across the SONET/SDH transport network. The first transport interface inserts a special latency instruction message into the Fibre Channel/FICON data before encapsulation in a GFP frame. After transport across the SONET/SDH network, the receiving second transport interface immediately sends the special latency instruction message back across the SONET/SDH transport network to the first transport interface which times the return of the special latency instruction message. From the time interval, the first transport interface can determine the latency of the SONET/SDH transport network and allocates the amount of buffers appropriately. This latency determination procedure is performed periodically so that the amount of allocated buffers can change as the latency of the SONET/SDH transport network changes.