Thousands of litres of hazardous waste spilled at a Fonterra plant in Southland early this morning.

Emergency services were called to the Edendale factory just after 2am when staff reported 5000-litre tanks of nitric acid and caustic alkali were overflowing.

Fire Service assistant area commander Dean Chalmers said the tanks were overflowing into a specifically designed catchment area but staff were concerned about the danger of the chemicals mixing and reacting together.

Nitric acid and caustic alkali are used to clean milk tankers and inside the factory.

"All the safety systems at Fonterra have kicked into gear. The bounded area has successfully contained the two chemicals and there hasn't been any chemical mixing at all," Chalmers said.

No one was hurt by the chemical release.

Firefighters and Fonterra staff were now making the scene safe and removing the chemicals from the bunded area.

Fonterra was investigating the cause of the spill but a machine malfunction may have caused multiple tanks to overflow, he said.