There have been various analyses of the efficiency of container port (or terminal) production using Data Envelopment Analysis (DEA) based on cross-sectional data. When time is not considered, the efficiency results derived using this approach can be biased. In order to overcome this problem, this paper applies DEA windows analysis, utilising panel data, to a sample of the world’s major container ports in order to deduce their relative efficiency. The results suggest that estimates of container port efficiency fluctuate over time. The paper concludes that existing programming methods for estimating efficiency are inadequate in capturing the long-term increased efficiency and competitiveness that accrue from significant investments.