KEY WEST, Fla. — For more than 24 hours last September, a Coast Guard helicopter and speedboat pursued drug traffickers and their contraband across the Caribbean Sea. Finally they caught up with the improbable vessel, the latest innovation in the decades-old drug war. It was a submarine.

The low-slung, diesel-propelled vessel, painted a dark shade to blend with the water, was believed to be carrying several tons of cocaine. But after the submersible’s crew scuttled the vessel and abandoned ship, the Coast Guard was able to salvage only two 66-pound bales of narcotics.

This is the new challenge faced by the United States and Latin American countries as narcotics organizations bankroll machine shops operating under cover of South America’s triple-canopy jungles to build diesel-powered submarines that would be the envy of all but a few nations.

After years of detecting these craft in the less trafficked Pacific Ocean, officials have seen a spike in their use in the Caribbean over the last year. American authorities have discovered at least three models of a new and sophisticated drug-trafficking submarine capable of traveling completely underwater from South America to the coast of the United States.