"We shared information with the Mexican navy, but the Mexican navy acted alone in actually executing the seizure," Chertoff told a news conference in Mexico City.
Mexican navy Vice Adm. Jose Maria Ortegon said the 30-foot (10-meter) green submarine was equipped with GPS and a compass, and its crew had planned to drop off its shipment on Mexican shores. The navy has since stepped up patrols in the area.
Authorities arrested four Colombian crew members who claim to be fishermen forced by drug cartels to move the cargo. They say they left the Colombian port of Buenaventura about a week ago.
Similar makeshift submarines carrying drugs have been discovered off Colombia and Central America, but the navy says the seizure is a first for Mexico.
Chertoff, who is on a three-day trip to meet with Mexican security officials, said drug cartels are increasingly relying on the subs to smuggle cocaine to the United States.
U.S. officials say traffickers use the vessels to carry about 32 percent of the cocaine moved by water from South America to the U.S.
Costing about US$1 million, the boats are usually painted to blend in with the color of the water, U.S. Coast Guard Cmdr. Thad Allen told reporters in Washington on Friday.
Many are capable of carrying more than 10 tons of cocaine and can be operated by remote control from hundreds of miles away, Allen said.
Drug cartels have been looking for new ways to move drugs north to the United States as the Mexican government cracks down on drug trafficking across the country.
