Abstract: Disclosed is a multi-level container storage system including a storage module including racks for storing containers, and a high-bay container storage. At least two tracks arranged in a first distance from each other in the vertical direction. The system includes a container handling apparatus capable of moving at least one container in three directions. The container handling apparatus includes a stacker crane including a carrier support for a carrier device of the container handling apparatus. The carrier device includes a handling mechanism for gripping, lifting, lowering, and releasing at least one container and is arranged to be moved out of and into the stacker crane, and into and out of the storage module, respectively, along one of the tracks of a rack, wherein the handling mechanism is arranged to move at least one container at most the first distance.