A system and method for controlling an engine control an EGR cooler bypass valve to divert at least a portion of EGR flow around an EGR cooler when operating under cooler fouling/plugging conditions, such as during idle, off-idle, exhaust system warm up and DPF regeneration or other post injection operation with EGR gas temperature below a corresponding threshold or with EGR low-temperature coolant temperature below a corresponding threshold. The system and method reduce exhaust gases passing through the EGR cooler that contain a high concentration of unburned or partially unburned fuel when the temperature in the EGR system is lower than the fuel condensation temperature.