Col. Rene Osorio says officials believe the vessel was carrying a total of 5.5 tons (5 metric tons).
The submarine-like craft is floating about 15 meters (50 feet) under the surface because the crew tried to sink it.
Osorio said Thursday divers will need another two days to recover all the cocaine.
A U.S. Coast Guard patrol detected the vessel Wednesday off the coast of the sparsely populated province of Gracias a Dios, near the Nicaraguan border. Five crew members were detained.