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President Calderon has deployed 45,000 federal troops and police to combat the drug gangs, yet in the midst of this crackdown, the Sinaloa cartel is flourishing. It's the largest, oldest and richest in Mexico. Yesterday on the program, an NPR investigation found strong evidence of collusion between the Mexican army and the Sinaloa cartel in the violent city of Juarez.

Today, we go to Mexico City to further explore whether corrupt elements within Calderon's government are somehow protecting one drug cartel while battling the rest.

NPR's John Burnett reports.

(Soundbite of traffic)

JOHN BURNETT: Here in Mexico City, people say it's an open secret that their government's vaunted war against the drug cartels is a rigged fight. Standing in the colonial heart of downtown Mexico City with me is a young man.

Unidentified Man: (Speaking Spanish)

BURNETT: He says the Mexican government is protecting one of the drug cartels. And he should know, he spent five years working as a federal police officer in Mexico City and left the force recently.

Unidentified Man: (Speaking Spanish)

BURNETT: He claims the government is attacking all the other drug mafias except the Sinaloa cartel, whose boss is Joaquin "El Chapo" Guzman, the world's most wanted drug lord. His home base is the Pacific coastal state of Sinaloa, known as Mexico's Sicily. It's the premier narco state, with a long coastline for smuggling cocaine from South America and rugged mountains to hide cannabis crops.

Manuel Clouthier, congressman from Sinaloa and a member of the president's own party, is deeply frustrated by his country's drug war.

Mr. MANUEL CLOUTHIER (Congressman, Sinaloa): (Through translator) The Calderon government has been fighting organized crime in many parts of this country, but has not touched Sinaloa. I know this. I'm Sinaloan. My family lives in Sinaloa. It's like we're trimming the branches of a tree when we should be tearing it out by the roots.

I believe that much of the problem of not combating a certain cartel in a certain state has much to do with corruption and lack of will.

BURNETT: We wanted to find out if Sinaloans are in fact untouched. NPR analyzed thousands of press releases on the federal attorney general's website, from the day Felipe Calderon assumed the presidency in December 2006, up to last week. We looked for every person the government arrested, prosecuted or sentenced who's associated with one of the seven major drug cartels.

What we found is that the Mexican government crackdown has not hit the Sinaloans as hard as they're saying. Forty-four percent of all cartel defendants are with the Zetas and the Gulf cartel. Only 12 percent of the defendants are with Chapo's organization. The numbers contradict the Mexican government, which claims it has arrested twice the percentage of Sinaloa gang members. Our database analysis is available at NPR.org.

We showed it to Congressman Michael McCaul. He's a Republican from Texas and a former federal prosecutor who sits on the Homeland Security Committee.

Representative MICHAEL MCCAUL (Republican, Texas): But I think that you've identified an issue of concern. And that is, why is the Sinaloa doing so much better than the others and why has the Sinaloa cartel been the one that has escaped a lot of the prosecutions compared to the other cartel members?

BURNETT: In response to NPR's findings, yesterday, the Mexican interior secretariat said all drug cartels are being, quote, "attacked proportional to their size." A spokesman rereleased figures they put out three months ago. He said 72,000 persons have been arrested for drug crimes in three years. NPR only counted federal arrest records of named cartel associates.

The growing criticism in Mexico that President Calderon is selectively fighting the cartels prompted him to speak out at a press conference in February.

President FELIPE CALDERON (Mexico): (Through translator) These accusations are totally unfounded, false. In most cases it reflects a misunderstanding of the facts, the result of other interests. I want to be clear.

BURNETT: Calderon went on to name several Sinaloa crime bosses they've arrested, the biggest being Vicente "El Mayito" Zambada, the son of a close ally of Chapo's.

NPR's analysis is supported by a Mexican law professor and organized crime expert, Edgardo Buscaglia. He teaches at ITAM, a Mexico City university, and at Columbia University in New York. Buscaglia has done his own analysis of arrests for the various cartels.

Professor EDGARDO BUSCAGLIA (Law, ITAM): If you look at the main organized crime group in Mexico, that is the Sinaloa confederation, it has been left relatively untouched.

BURNETT: Senior U.S. officials declined to speak on the record for this report. They stressed that they believe Calderon is sincere about rooting out corruption in his government and taking down all the drug mafias.

The United States is giving $1.3 billion in military and justice aid to Calderon to help him defeat the cartels.

A senior State Department official on background acknowledged that Calderon has to prioritize his targets. A DEA official added: Calderon is hitting the Zetas the hardest because they are the most brazen in committing murder, kidnapping and extortion.

But does the Sinaloans' reputation for well-placed bribes help keep them out of jail? Jorge Carrasco covers organized crime for the respected Mexican newsmagazine Proceso, which recently put Chapo on the cover with the headline "The Untouchable."

Mr. JORGE CARRASCO (Reporter, Proceso): (Through translator) A cartel cannot flourish at their level without civil and military protection at the highest levels.

BURNETT: The Sinaloans are widely regarded as the most sophisticated cartel at transportation, intelligence gathering and bribery. Last year, Proceso reported on how a Sinaloa faction controlled several airports around the country through a network of corrupt federal agents. They even had their own hangar at the international airport in Mexico City.

Just last week, the newspaper Reforma described how the Sinaloans had thoroughly infiltrated the federal police. The drug gang knew where the cops were being sent next and how many buses would carry them. A Navy investigation revealed the Sinaloans controlled eight seaports for cocaine smuggling from South America.

Then there's the 2007 army intelligence report, obtained by The Wall Street Journal and shared with NPR. It describes how Chapo would visit his marijuana ranch in Sinaloa, quote, "in caravans of six vehicles, with the protection of the Mexican army."

Again, Congressman Michael McCaul.

Rep. MCCAUL: Has the Sinaloa infiltrated the Mexican government? Absolutely. Have they infiltrated the Mexican military? Absolutely. Calderon's got a very difficult job of trying to root out corruption within his own ranks.

BURNETT: NPR's data analysis found 400 public officials, from local cops to army officers, who have been arrested for working for the drug mafias in the last three and a half years. The pattern is clear: All the cartels infiltrate local and state agencies, but the Sinaloans and their former allies are more likely to pay off the military and senior federal officials.

Again, law professor and organized crime analyst Edgardo Buscaglia.

Prof. BUSCAGLIA: The Sinaloa has been clearly the winner of all that competition among organized crime groups. And as a result of that, they have gained more economic power, they have been able to corrupt more, corrupt with more frequency and corrupt with more scope. And now you see that Sinaloa is the most powerful criminal group not just in Mexico, all over Latin America.

BURNETT: Since bribing his way out of a maximum security prison in a laundry truck in 2001, Chapo Guzman is the second most wanted fugitive in the world, after Osama bin Laden. They're both protected by mountains, native cunning and informers.

A former senior DEA official with experience in Mexico concedes that Chapo has effectively penetrated every civilian and military force in Mexico. The former agent said he knows of a Mexican general who once tried to catch the elusive drug lord. The general was up against enormous obstacles, he said. Every time he got close, his own men would tip off Chapo.

John Burnett, NPR News.

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