In food processing and similar types of industries, packaging is performed in two steps, namely "primary packaging" and "secondary packaging". Generally the placement of the product on the pallets is done using custom designed mechanisms and conveyor systems. The desire for flexibility in such systems, produced robotic palletizing/collation systems. These systems usually include a cell incorporating a two-dimensional linear motor. This paper presents the development of an adaptive control for this type of linear motor. For this aim, first the modeling of the linear motor has been completed. After deciding on the best model, an adaptive controller has been suggested to improve the reliability of the system.