The arrests mark the first time U.S. authorities have captured and charged Al Qaeda suspects in a drug trafficking plot in Africa.
The three suspects — believed to be in their 30s and originally from Mali — were arrested by local authorities in Ghana earlier this week and turned over to U.S. agents.
They arrived in the United States early Friday morning, officials said, and were ordered held without bail after a brief court appearance later in the day in which they did not enter pleas to charges of narcoterrorism conspiracy and conspiracy to provide material support to terrorists.
Michele Leonhart, the head of the Drug Enforcement Administration, said the case shows a "direct link" between Al Qaeda and drug traffickers.
The U.S. has long been concerned about close ties between militants and the heroin trade in Afghanistan. But the African case appears to show an expansion of both Al Qaeda's illegal activities around the globe and American efforts to curtail black market deals that funnel cash to spur terror operations.
The four-month investigation was also the third time in recent years that the U.S. has targeted transnational suspects in an elaborate sting using informants posing as South American narcoterrorism operatives.
U.S. attorney Preet Bharara said the charges show "the emergence of a worrisome alliance between Al Qaeda and transnational narcotics traffickers.
As terrorists diversify into drugs, however, they provide us with more opportunities to incapacitate them and cut off the funding for future acts of terror."
Authorities say the men are associates of Al Qaeda's North African branch, and told DEA informants that Al Qaeda could protect major shipments of cocaine in the region, driving the drugs by truck through the Sahara desert before eventually bringing them to Spain.
A criminal complaint unsealed Friday charges that Oumar Issa, Harouna Toure, and Idriss Abelrahman worked with Al Qaeda in the Islamic Magreb.
Court papers say Toure and Abelrahman at one point claimed the profits from the drug business "will go to their people to support the fight for 'the cause'."
Court papers say the DEA infiltrated the group by using informants posing as supporters of Colombia's rebel army, the Revolutionary Armed Forces of Colombia, or FARC, which the U.S. government considers a terrorist organization.
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