Around five tractors gathered outside the TotalEnergies refinery in Feyzin early on Monday morning as part of a demonstration organised by the agricultural union Coordination Rurale.
Video from the scene showed tractors unloading piles of waste near the refinery entrance while riot police monitored the protest. Tanker trucks were still able to enter and leave the site.
The protesters say higher diesel prices, rising fertiliser costs and falling cereal prices are putting severe pressure.
French farmers have staged repeated demonstrations in recent years over production costs, environmental regulations and competition from imports, arguing that many farms are struggling to remain profitable.