Abstract This paper addresses a loading problem with the objective of part movement minimization in an FMS with tool flexibility when a tool can perform multiple operations. The problem is formulated as a quadratic programming problem. The quadratic terms are linearized using the methods of Balas, and Glover and Woolsey, and the resulting 0–1 integer linear program is solved using Hyper LINDO. The problem is further extended to take into consideration the combined objective of part movement minimization and workload balancing. Numerical examples are presented to illustrate the problem environment and the solutions.