Abstract-FPGAs are promising candidates for computational tasks in space applications. However, they are susceptible to radiation-induced errors, the most common failure being due to the corruption of their configuration memory. Module-based partial reconfiguration and frame-based scrubbing are the two most commonly used techniques for detecting and recovering from configuration memory errors. Both methods require userdesigned reconfiguration controllers (RC) to read and write FPGA configuration memory data. This paper proposes a Programmable Configuration Controller (PCC) specifically designed for fault-tolerant applications. PCC has a soft Application Specific Instruction Set Processor (ASIP) architecture. The PCC is software programmable using the C language, which allows it to be used in a wide variety of fault-tolerant applications with minimal design and/or hardware overhead. PCC also has instruction extensions to accelerate commonly-used reconfiguration operations such as reading and writing configuration data. Through 5 case studies, we demonstrate that the use of an ASIP architecture for reconfiguration control in applications prone to radiation-induced corruption strikes the right balance between speed, resource utilization and flexibility.