Massive .50 caliber rifle was one of 19 weapons inside Mexican hideout.
Justice Department confirms it was sold through Fast and Furious program.
ATF sting involved deliberately selling weapons to Mexican cartel dealers.
Intention was that guns would then be tracked and used to make arrests.
But ATF was forced into admission that it lost 1,400 of the 2,000 guns sold.
It is not believed the weapon was used in shootout that left five of El Chapo's henchmen dead and injured one Mexican Marine.
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By CHRIS PLEASANCE FOR DAILYMAIL.COM
PUBLISHED: 09:06 EST, 16 March 2016 | UPDATED: 18:29 EST, 16 March 2016
The Justice Department has confirmed that a .50 caliber sniper rifled found at El Chapo's Mexican hideout and used to shoot down helicopters was sold through the Fast and Furious program.
The rifle was found inside the Los Mochis property where the Sinaloa Cartel kingpin was discovered hiding on January 8 this year before a raid by the Mexican Marines that led to his capture.
Fast and Furious was a botched Bureau of Alcohol, Tobacco, Firearms and Explosives smuggling operation in which guns were deliberately sold to cartel dealers.
The hope was that the weapons could be traced south over the border into Mexico, and then used to make arrests using serial numbers as evidence.
While the program did lead to a handful of arrests, the agency was eventually forced to admit that it lost track of 1,400 of the 2,000 weapons it sold
Officials say the rifle was among 19 weapons recovered from El Chapo's hideout in Sinaloa-controlled territory, and was the only one found to have been sold through the program.
According to earlier reports, the weapon would have been given to a sharpshooter positioned on a hill around El Chapo's hideout.
The hitman's job would have been to watch out for helicopters flying low over the ground in order to hunt for the cartel kingpin, and then take them out.
The rifle fires huge .50 caliber rounds, the same bullets fired by machine guns typically mounted on top of a Humvee, which are designed to penetrate reinforced glass, metal and concrete.
Fired using a bipod because of the extreme recoil, the rifles are used to disable cars by firing through the engine block, can take down helicopters, and are capable shooting through walls.
The Fast and Furious program was only uncovered when border patrol agent Brian Terry, 40, a former U.S. Marine, was killed in a shootout with cartel members in December 2010.
Two weapons found near to the scene of Terry's death were traced back to the operation, and were shown to have been bought by the Sinaloa Cartel - run by El Chapo.
While it is unclear whether either of the weapons were used to kill Terry, their very presence at the scene set off a political chain reaction that led to then-Attorney General Eric Holder being found in contempt by Congress for failing to turn over documents relating to the program.
Holder had previously stated that he had known about the operation for only a few weeks before Terry's death, but memos uncovered later showed he had been aware of it for at least a year.
Barack Obama has long been criticized over his handling of the political fallout after using executive privilege over the documents Holder was asked to release, preventing further prosecution.
In total, 34 of the 2,000 weapons sold under Fast and Furious were believed to be .50 caliber rifles of the kind found in El Chapo's hideout.
Joaquin 'El Chapo' Guzman, who escaped his cell at the Altiplano jail last July, was recaptured in a shootout earlier this month that killed five of his guards and injured one Mexican Marine.
The billionaire cartel leader was tracked to a property in Los Mochis after exchanging a series of romantic texts with actress Kate del Castillo which authorities were able to track.
He is now facing extradition to the U.S. for trial and almost certain imprisonment, having escaped from Altiplano, Mexico's most secure jail, twice before.
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