Interior Minister Jose Serrano announced the seizure on Twitter, posting pictures of rows, piles and bags of the dark-colored shark fins.
Shark fins are coveted in Asia for medicinal and cooking uses. Their trade is banned in Ecuador.
Ecuadorian authorities reported that at least 300,000 sharks were killed by the traffickers, in one of the most serious environmental crimes reported in the country in years.
The shark fins were seized in several operations in the port city of Manta. Police did not say how long ago the fins were harvested.