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High speed satellite communication networks are emerging as part of the future global wireless communication systems. However, existing transmission control protocols for satellite networks do not provide satisfactory performance over high speed satellite links due to their inefficient congestion avoidance algorithms. This paper identifies the reason for low throughput of a widely used protocol space communications protocol specification (SCPS) in such networks and proposes a new transmission control protocol (TCP) congestion avoidance algorithm to overcome the drawback of the congestion avoidance algorithm used in the SCPS protocol. Numerical results through simulations demonstrate that the proposed new algorithm can achieve significant throughput improvement over links with variable error rates, compared with its legacy counterpart.