Garda Superintendent Kevin English said the operation was uncovered during a planned search of a commercial unit about 3km from Malin town shortly before 10am.
Two men were arrested at the scene.
Supt English said the plants were at every stage of development and that a large quantity had already been harvested and was ready for market.
He said the find is very significant and an examination of the scene is on-going to determine the value of the plants.