Use of the Gaussian inverse Wishart probability hypothesis density (GIW-PHD) filter has demonstrated promise as an approach to track an unknown number of extended targets. However, when targets of various sizes are spaced closely together and performing maneuvers, estimation errors will occur because measurement partitioning algorithms fail to provide the correct partitions. Specifically, the sub-partitioning algorithm fails to handle cases in which targets are of different sizes, while other partitioning approaches are sensitive to target maneuvers. This paper presents an improved partitioning algorithm for a GIW-PHD filter in order to solve the above problems. The sub-partitioning algorithm is improved by considering target extension information and by employing Mahalanobis distances to distinguish among measurement cells of different sizes. Thus, the improved approach is not sensitive to either differences in target sizes or target maneuvering. Simulation results show that the use of the proposed partitioning approach can improve the tracking performance of a GIW-PHD filter when target are spaced closely together.