Marta Rita Velazquez, 55, worked for the state department between 1989-2002 and had top-secret clearance.
Authorities say she fled the US in 2002 amid reports a spy she had recruited was co-operating with investigators.
Ms Velazquez, who now lives in Sweden, is also accused of passing secret documents to the Cuban government.
If extradited, tried and convicted, she could face life in prison.
The charges stem in part from an earlier case against Ana Belen Montes, Ms Velazquez's alleged co-conspirator, who pleaded guilty in 2002 to spying on behalf of the Cuban government and is now serving a 25-year prison sentence in the US.
According to an indictment unveiled by the US justice department, Ms Velazquez recruited Montes in 1984, introduced her to the Cuban Intelligence Service and then helped her obtain a job at the US Defense Intelligence Agency. Montes became the agency's senior analyst for Cuban affairs.
Ms Velazquez is also accused of passing on documents and information to Cuban intelligence officials on matters relating to US national defence.
The indictment against Ms Velazquez, who has also gone by the names Marta Rita Kviele and Barbara, was first returned by a grand jury in 2004 but was not unsealed until Thursday.
She was born in Puerto Rico in 1957 and studied at Princeton University, Georgetown Law Center and Johns Hopkins University, the charge sheet says.
Ms Velazquez developed a close friendship with Montes at Johns Hopkins, US authorities said.
As a federal employee, Ms Velazquez worked for the state department's development arm, the US Agency for International Development, held a top-security clearance and was posted to US embassies in Nicaragua and Guatemala.
As it emerged that Montes had pleaded guilty to espionage and was co-operating with the US government, Ms Velazquez resigned her government job and left the US.
The US has maintained a near total trade embargo against Cuba since 1962, but during his first term in office President Barack Obama relaxed restrictions on Cuban Americans' travel to the island and raised the limit on the amount of money they could send to family members there.