"Today's allegations reflect the emergence of a worrisome alliance between al-Qaeda and transnational narcotics traffickers," US Attorney Preet Bharara said.
The accused identified as Oumar Issa, Harouna Toure and Idriss Abelrahman were flown to New York on Friday, Dec 18 after they were arrested in Ghana on Dec 16.
Prosecutors said that they funding three US banned-terrorist organization, al-Qaeda; al-Qaeda in the Islamic Magreb and the Fuerzas Armadas Revolucionarias de Colombia (FARC), the world's largest supplier of cocaine.
The trio were arrested in a sting operation in which they agreed to transfer hundreds of kilograms of cocaine through West and North Africa.
The operation was jointly carried out by federal prosecutors in New York and agents at the Drug Enforcement Administration in the United States and Ghana.
"It is the first time associates of al-Qaeda have been charged with "narco-terrorism offenses," the Justice Department said.