Muhammad Sallam Spawi, an officer in Sabah state on Borneo island, says police surprised four smugglers as they were unloading bags of eggs Sunday. But he says the men managed to flee in their boat.
Still, he said Tuesday the seizure was "the biggest ever" in Sabah.
He said the men were speaking Tagalog, which is spoken in the Philippines.
Abdul Karim Dakog, an officer with the state wildlife department, says the department hopes the eggs, from the endangered green and Hawksbill turtles, may still hatch in a conservation area.
Trade in turtle eggs is illegal in Malaysia but the eggs remain popular in local food markets. They cost about 80 cents each.