North Korea and Iran are the only other countries that have been assigned so-called "mission managers", who supervise intelligence operations against them.
In a statement released on Friday, the office of John Negroponte, the natioinal intelligence director, said the manager would be responsible "for integrating collection and analysis on Cuba and Venezuela across the intelligence community" and "ensuring the implementation of strategies" that have not been disclosed.
"Such efforts are critical today, as policymakers have increasingly focused on the challenges that Cuba and Venezuela pose to American foreign policy," the statement said.
The director's office said the manager would also be asked to ensure "that policymakers have a full range of timely and accurate intelligence on which to base their decisions".
The document did not say what kind of decisions US officials could be making with regard to either country.
The statement said that J Patrick Maher, whose previous job was deputy director of the CIA's office of policy support, will assume the role temporarily until a permanent candidate is found.
His biographical sketch supplied in the announcement indicates he was one of the architects of the CIA's current counterterrorism strategy in Colombia and managed the agency's operations in the Caribbean basin.
Hugo Chavez, the Venezuelan president, said he believed that Maher's appointment was linked to presidential elections due in December that he is widely expected to win.
"This shows us that the empire does not rest, that it is hatching a plan for December or a period before December," he told reporters. "But whatever it is, we will thwart it."