Method to prevent firmware defects from disturbing logic clocks to improve system reliability

A computer implemented method and data processing system are provided for preventing firmware defects from disrupting logic clocks. In response to a firmware interface requesting a scan operation for a functional unit, protection logic allows a scan enable to activate to the functional unit only if the logic clocks are stopped to that functional unit, otherwise the scan enable is not activated, an error is indicated, and an interrupt is presented to firmware. Also, in response to a command from a firmware interface to stop the logic clocks to a functional unit, protection logic allows the clocks to be stopped to the functional unit only if the functional unit is already indicating a catastrophic error, otherwise the clocks are not stopped, an error is indicated, and an interrupt is presented to firmware.