A semi-submersible vessel capable of transporting between 10 and 15 tons of drugs was found under construction in the Gulf of Guayaquil, the Ecuadorian navy said.
The sub is related to a similar vessel that was scuttled by its crew to avoid capture in January, the navy said.
The semi-submersible, which is 15 meters (49 feet) long by four meters (13 feet) wide, was 70 percent complete.
The vessel has four compartments, including one in the bow for ballast, a large storage area, an engine room and a fuel bunker.
"The apparatus was located in a strategic sector of the Gulf, allowing it, once completed, to easily enter the open sea without being detected," the navy said in a statement.
The vessel was hidden in dense vegetation and covered with mud to make it difficult to detect by air or sea, the navy said.
The sub was found around midnight Monday on a small island between the Verde and Escalante islands during a joint operation conducted by the navy, coast guard, marine corps and Guayaquil port authority.
Drug enforcement agents seized a semi-submersible capable of hauling up to 14 tons of drugs and housing a crew of five or six in July 2010 in the coastal province of Esmeraldas, which borders Colombia.
The sub had the capacity to carry drugs to Mexico that were eventually bound for the United States.
In May 2010, drug enforcement agents found a homemade semi-submersible apparently used to smuggle drugs and arrested four people.
The 15-meter (49-foot) vessel was discoverd at a shrimp farm in El Oro, a province in southern Ecuador, during a joint operation by two elite police units.
The sub had the capacity to carry at least four tons of drugs and may have been built to smuggle cocaine into Mexico for the U.S. market.
The custom-built semi-submersibles, similar to a submarine, operate with a significant portion of their hulls below the waterline, making it difficult to detect them.
Colombian drug traffickers started using semi-submersibles in 1993. In that year, Colombia's navy seized one of the vessels off Providencia Island in the Caribbean.
The semi-submersibles cannot dive like a normal submarine, but they are equipped with a valve that, when opened by the operators, quickly floods and scuttles the vessel, causing it and any drugs on board to quickly sink to an unrecoverable depth.
The crew then jumps overboard and, since no drugs are discovered, they avoid prosecution. EFE