One of the main goals of fault injection techniques is to evaluate the fault tolerance of a design. To have greater confidence in the fault tolerance of a system, an accurate fault model is essential. While more accurate than gate level, transistor level fault models cannot be synthesized into FPGA chips. Thus, transistor level faults must be mapped to the gate level to obtain both accuracy and synthesizability. Re-synthesizing a large system for fault injection is not cost effective when the number of faults and system complexity are high. Therefore, the system must be divided into partitions to reduce the re-synthesis time as faults are injected only into a portion of the system. However, the module-based partial reconfiguration complexity rises with an increase in the total number of partitions in the system. An unbalanced partitioning methodology is introduced to reduce the total number of partitions in a system while the size of the partitions where faults are to be injected remains small enough to achieve an acceptable re-synthesis time.