Especially for Indonesia as the largest archipelago nation in the world, efficiency logistics systems and their connection to global logistics is a key role to the success. Free trade agreement in the ASEAN region leads to more competitive market in the container shipping industry. The increasing demand does not reduce the competition; on the contrary, ports and terminals compete harder for their customers, the shipping lines. This study compares the efficiency of port operations for the Indonesian Major Port and Selected Southeast Asia port. This study use Data Envelopment Analysis to evaluate efficiency performance of the container ports and employ several scenarios adapted from multi and total factor productivity concept. Sensitivity analysis aimed to determine which factors are more critical for efficiency improvement. The conclusion of this study provides reasonable theoretic support for port managers to improve management strategies.