The Associated Press
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.
President Felipe Calderon has deployed 25,000 soldiers across the country to battle drug gangs, which have responded with bold attacks on the military and police. More than 4,000 people have been killed in turf wars, assassinations and shootouts since Calderon took office in December 2006.
Chertoff said Friday that a US$400 million aid package recently approved by the United States would go to help Mexico buy equipment, train agents and coordinate information with the U.S. He also praised Mexico's drug offensive.
"My personal belief is that you got to step down very hard very quickly on those people who challenge the rule of law and defy it, and that's why I'm pleased to see the Mexican military has been involved," Chertoff said. "They have been aggressive, and most of all they haven't been intimidated."
Associate Press writers E. Eduardo Castillo in Mexico City and Eileen Sullivan in Washington contributed to this report.