This paper describes a study which investigated the influence that alternate operations might have on the performance of flexible manufacturing systems (FMS). An alternate operation might be directed, for example, to avoid a long queue and would, perhaps, be performed by a machine of leaser capability so that a time penalty would be incurred. Three schemes for implementing alternate operations within the hierarchical structure of the FMS are devised and test results are compared with the performance achieved using no alternate operations. Results show that alternate operations can reduce flow (cycle) time (and therefore in-process inventory) while increasing machine utilization. The most effective of the three schemes requires use of multiple levels of the control hierarchy, applying a linear programming model to prescribe production plans and adaptive control to implement the plans over time.