OTAY MESA, Calif.—The federal agents who spend their days hunting for tunnels used to smuggle marijuana from Mexico know the subtle signs of an illegal passageway hidden amid the labyrinth of warehouses in this border community just outside Tijuana.
They know large tunnels cost about $1 million apiece to build and can take up to nine months to finish. They know the suspected cartel kingpin allegedly behind the most sophisticated passageways—including one with an electrified rail system—that have been popping up on the border at an alarming rate.

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A Homeland Security special agent crawled through a drug tunnel in Otay Mesa, Calif., on Nov. 4, 2010. The tunnel was found by agents at a warehouse near the U.S.-Mexico border. Sandy Huffaker/Getty Images
But a stubborn mystery remains at the heart of the drug-tunnel phenomenon: the identities of the people who designed and built these engineering feats.
As border agents focus on investigating and dismantling networks that fund and use the tunnels, tracking down the engineers is crucial, federal agents said.
"I would liken that to winning the law-enforcement lottery," said Derek Benner, the special agent in charge of investigations for U.S. Immigration and Customs Enforcement in San Diego. "These guys would just be a wealth of information for us."
Drug smugglers have been burrowing under the border for two decades. Since 1990, 159 tunnels have been discovered crossing into the U.S. from Mexico. Construction boomed as border security tightened, forcing smugglers underground. In the past four years, the building of illegal tunnels increased by 80%, according to 2012 federal report.
The most recent was discovered in Tecate, Mexico—about 35 miles east of San Diego—by Mexican army officials in December. It crossed into California but an exit hadn't been built yet, federal officials here said.

In the last two years, federal agents in San Diego have seized about 100 tons of pot from secret tunnels dug under the border to Mexico. In this 2010 video, a federal agent gives a tour of one of these drug tunnels. (Photo: ICE)
The tunnels are primarily used to smuggle pot into the U.S., but U.S. Homeland Security officials say the passageways pose a "significant security vulnerability" and could also be used to smuggle weapons or cash across the border. Most are found in Arizona and California, though a large number are just rudimentary holes, or tap into existing cross-border drainage systems.
The most sophisticated tunnels tend to pop up in Otay Mesa, a busy border outpost that is part of San Diego, where the clay-like soil allows for larger and deeper passages and warehouses help conceal tunnel exits. The tunnels are often more than 1,000 feet long, shored up with concrete or wood, and equipped with ventilation systems, phones, lighting, and in one, an electric rail system capable of pushing tons of pot under the border at about 20 miles per hour.
The tunnels typically begin in a home in Mexico, run under the border fence and emerge in a warehouse district used to store products for legitimate cross-border trade. Border agents usually find them by watching warehouses on the U.S. side for activity that seems abnormal, such as late-night work shifts, or trucks parked out front that never seem to move.
In 2009, they discovered one beneath a false bathroom floor built onto a hydraulic lift that descended 90 feet below ground. "It was an engineering marvel," said Jerry Conlin, a U.S. border-patrol agent, who said the tunnel had ventilation, lighting and a phone. After a tunnel is discovered, federal officials fill it with concrete slurry to close it, he said.
Federal agents believe the architects come from Durango, a mining industry state in northern Mexico. They believe there is a small group of trusted engineers—who are highly valued and guarded by the drug lords employing them—responsible for designing and overseeing the construction of the tunnels.
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Federal officials say they know of just one architect who was arrested and prosecuted in the U.S.: Felipe de Jesus Corona-Verbera, who built one of the first sophisticated tunnels discovered at the border, a 200-foot-long passage from Mexico into Arizona used to funnel cocaine. It was discovered in 1990 and Mr. Corona-Verbera eluded authorities for more than a decade until he was arrested in 2003. He was sentenced to 18 years in prison in 2006, according to federal records, and is currently in prison outside Tucson.
"If you have an engineer who's building you really good tunnels, you'll protect that commodity," said Tim Durst, the assistant special agent for Immigration and Customs Enforcement, who leads a tunnel task force here. "It's the most important commodity you have."
In the past two years, agents in San Diego seized about 100 tons of pot with a conservative estimated value of around $60 million from various tunnels. In that time, prosecutors have won 20 convictions in connection with tunnels on the San Diego border, said Sherri Walker Hobson, the assistant U.S. attorney for the Southern District of California.
Federal prosecutors in San Diego are calling on Mexico to extradite Jose Sanchez-Villalobos, after a grand jury indicted him last year on 13 counts of drug smuggling and allegedly financing construction of two of the largest tunnels on the border, including one dubbed the Marconi tunnel. Prosecutors say Mr. Sanchez-Villalobos is a high-ranking member of the Sinaloa drug cartel. His lawyer, Guadalupe Valencia, said Mr. Sanchez-Villalobos denies the charges and is fighting extradition.
Despite those successes, investigators here and in Mexico have struggled to find the engineers. Investigators believe they know the identity of one, Mr. Durst said, "but we hit several roadblocks in locating that person."
Officials are perplexed about how the engineers manage to be so precise in constructing a tunnel to emerge at exactly the right spot in the U.S. Mr. Durst believes they use compasses to help guide the work, but he is curious about how they manage without a global-positioning device, which won't work underground.
"There are so many questions," Mr. Durst said. "What are their techniques? How the heck do they build these things so well?"
Write to Tamara Audi at tammy.audi@wsj.com