I must say I was a bit shocked to read the words Leon Panetta used before Hillary Clinton during a National Security meeting in June 2011, as reported in the April 14 issue of the New York Times Magazine: "No, Hillary, it's you who are flat wrong."
To be sure, Panetta is a tough nut of a politician, but these are strong words coming from the head of an intelligence agency (as Panetta then was) to a Secretary of State. The latter is the highest ranking executive branch official in the presidential line of succession and the order of precedence (as Alexander Haig once too hastily pointed out).
The issue was who was in charge of the drone program being conducted over Pakistan, the ambassador, Cameron Munter (who was present by video link) or the Station Chief. Specifically, Munter wanted to have approval power over the drone strikes. Hillary agreed. Panetta insisted otherwise.
The exchange was recounted by Mark Mazzetti in a chapter reprinted from his new book, The Way of the Knife: the CIA, a Secret Army, and a War at the Ends of the Earth (Penguin Group, 2013). The article continues:
There was a stunned silence and National Security Council Adviser Tom Donilon tried to regain control of the meeting. In the weeks that followed, Donilon brokered a compromise of sorts: Munter would be allowed to object to specific drone strikes, but the CIA could still press its case to the White House and get approval for strikes even over the Ambassador's objections. Obama's CIA had, in essence, won again.
This kerfuffle points up the ambiguous relationship that exists between an ambassador and a Station Chief and why great care must be taken to preserve the relationship. While an Ambassador is often from the State Department, he does not represent the State Department. He represents the president, and therefore he has to look after the needs of all the agencies.
The Station Chief has his own channel of communications and with it the statutory obligation to protect CIA sources and methods. The CIA, unlike in the British system, does not have a subordinate role to the State Department. It is beholden to the National Security Council and the President. And thereby hangs the ambiguity: the CIA is independent of the State Department in Washington (although the Secretary of State and the Secretary of Defense are the only two statutory members of the National Security Council.) And yet the Ambassador out in the field is in charge of United States activities that take place in his country of accreditation.
Often with the advent of a new administration in Washington, the new president sends a letter to ambassadors reminding them that they are in charge of what goes on in terms of American activities in their country of assignment. In one instance, an ambassador called in the Station Chief and informed him that, in view of the president's letter, he henceforth wanted to see all messages that were sent out by the station. It was obviously a power play, and the Station Chief, while not objecting, simply ignored the ambassador's demand.
An ambassador can send a CIA Station Chief home if he so deems necessary, but it likely would be at the expense of his credibility with the CIA and the intelligence community.
The bottom line is that the imperative is to get along. And after nearly 70 years of the CIA's existence, the "getting along" works better than it did in the early years.