It took six firecrews to fight the blaze after being called following reports of explosions at the plant.
Merseyside Fire & Rescue Service said the fire had started in a silo containing 10 tonnes of sawdust product.
“Around 150m³ of the tank was severely damaged by fire,it said.
Fire protection staff at Sonae worked with firefighters to help prevent the fire from spreading.
The Knowsley plant has only just recovered from a major fire last summer, which shut down raw particleboard production for six months.
Health & Safety Executive has launched an investigation.
