Debate over the issue reignited last month, as Armitage and then-Secretary of State Colin L. Powell departed and Condoleezza Rice prepared to replace him, said an administration official familiar with the matter. When the Pentagon refused to change language in the execute order, that put the issue before Rice.
In the past week, however, she has made it clear that she intends to protect the existing chief-of-mission authority. "Rice is resolute in holding to chief-of-mission authority over operations the way it exists now, for a very rational reason -- you need someone who can coordinate," said a senior State Department official.
Some officials have viewed the debate as an early test of how Rice will defend State Department views on a range of matters in bureaucratic infighting with the Pentagon.
The State Department's concerns are twofold, officials said: Conducting military operations would be perilous without the broad purview and oversight of the U.S. ambassador, and it would set a precedent that other U.S. agencies could follow.
"The chief-of-mission authority is a pillar of presidential authority overseas," said the administration official familiar with the issue. "When you start eroding that, it can have repercussions that are . . . risky. Particularly, military action is one of the most important decisions a president makes . . . and that is the sort of action that should be taken with deliberation."
U.S. ambassadors have full responsibility for supervising all U.S. government employees in that country, and when granting country clearances they are supposed to consider various factors, including ramifications for overall bilateral relations. For example, one reason the U.S. military never conducted aggressive operations against al Qaeda in Pakistan was a fear that such actions would incite the local population to overthrow the fragile, nuclear-capable government of President Pervez Musharraf.
The rift between the Pentagon and State Department over chief-of-mission authority parallels broader concerns about the push to empower the Special Operations Command in the war on terrorism. The CIA, for example, has concerns that new intelligence-gathering initiatives by the military could weaken CIA station chiefs and complicate U.S. espionage abroad.
Without close coordination with the CIA, former senior intelligence officials said, the military could target someone whom the CIA is secretly surveilling and disrupt a flow of valuable intelligence.