The alleged conspiracy involved the Fuerzas Armadas Revolucionarios de Colombia, or FARC, which has been designated a foreign terrorist organization by the United States.

“Today’s indictment reflects DEA’s commitment to securing our nation and protecting our citizens” Ms. Leonhart said. “These charges reveal how Indjai’s sprawling drug and terror regime threatened the national security not only of his own country, but of countries across the globe.

“As the head of Guinea-Bissau’s Armed Forces, Indjai had insider access to instruments of national power that made him an allegedly significant player in West Africa’s dangerous drug trade,” she said.

“Partnering with individuals he believed to be part of a terrorist organization like the FARC served to expand Indjai’s criminal activities and the damage he could cause.”

An indictment alleges that Mr. Indjai conspired to use his power and authority to be a middleman and his country to be a way-station for people he believed to be terrorists and narcotics traffickers so they could store, and ultimately transport narcotics to the United States, and to procure surface-to-air missiles and other military-grade hardware to be used against U.S. troops.

According to the indictment, Mr. Indjai became the head of the Guinea-Bissau armed forces in June of 2010.

Beginning in the summer of 2012, he and his co-defendants communicated with confidential sources working with the DEA who purported to be representatives or associates of FARC.

The indictment said the communications occurred by telephone, email and in a series of audio-recorded and videotaped meetings over several months in Guinea-Bissau.

The indictment said that during meeting in Guinea-Bissau beginning in June 2012, Mr. Indjai and his associates agreed to receive and store multiton shipments of FARC-owned cocaine in Guinea-Bissau; to receive the cocaine off the coast of Guinea-Bissau; and to store the cocaine in storage houses pending its eventual shipment to the United States, where it would be sold for the financial benefit of the FARC.

It said Mr. Indjai and the others also agreed that a portion of the cocaine would be used to pay Guinea-Bissau government officials, including Mr. Indjai, for providing safe passage for the cocaine through Guinea-Bissau.

Mr. Indjai has been charged with one count of conspiracy to engage in narcoterrorism; one count of conspiracy to distribute five kilograms or more of cocaine, knowing or intending that the cocaine would be imported into the United States; one count of conspiracy to provide material support and resources to an terrorist organization; and one count of conspiracy to acquire and transfer anti-aircraft missiles.

He faces life in prison if convicted.