Space debris tracking during atmospheric re-entry is a very complex problem due to high variations with time of the ballistic coefficient. The nature of these variations is generally unknown and an assumption has to be made in the estimation model which can result in high model errors. An estimator which is robust against model errors is therefore required. In previous work done by the authors, Moving Horizon Estimation (MHE) has been shown to outperform other classical nonlinear estimators in terms of accuracy and robustness against poor initialization for a simplified 1D case of space debris tracking during the re-entry. However, the large computation time of the MHE prevents its implementation for the 3D cases. Recently, the Moving Horizon Estimation with Pre-Estimation (MHE-PE) which requires much less computation time than the classical MHE while keeping its accuracy and robustness has been proposed. This paper therefore implements the MHE-PE to solve the 3D space debris tracking problem during the re-entry. Its performances are compared to some classical nonlinear estimators in terms of non-divergence percentage, accuracy and computation time through Monte Carlo simulations.