SHOULD THE PENTAGON continue to run the National Security Agency and the National Reconnaissance Office? Or should it yield up these multibillion-dollar intelligence-collection agencies (communications and satellites, respectively) to the Director of Central Intelligence? We are dealing here with something more than the usual epic bureaucratic struggle for territory. The real issue is whether, for the first time since the intelligence community was organized in 1947, the President will actually control the whole of it. Similarly, will the Senate Intelligence Committee, and any future House counterpart, actually oversee the whole of it? For without centralization, the President will remain poorly placed to prevent gross abuses of the sort whole disclosure led to the current review, and to get the kind of intelligence he needs to conduct national policy. And the Congress will be unable to conduct effective oversight.

Look at it this way: Currently the Pentagon, condition to scan the world for military threats, controls NSA and NRO. But are these agencies being assigned the right tasks, and only those tasks that are really necessary? And are their findings properly evaluated and used? Remember, we are talking about fully 80 per cent of the intelligence budget. Somebody, it seems to us, ought to be taking into account not only the theoretical military threat but also the political adversities - and realities - that help shape and define the military threat in practical terms. Somebody ought to be conveying to the government's intelligence chief (in this case, the Director of Central Intelligence) the questions on the mind of the chief civilian policy maker. And, frankly, we don't see who else but the President can perform this role as ultimate taskmaster of all branches of intelligence collection and analysis.

Pentagon opponents of consolidation suggest it will rob the President of dissent in the intelligence-estimating process. This is well worth worrying about but it is not a likely result of the step at hand. There are other ways, including sensible leadership and strict rules of procedure, for building protection of independent thinking and dissent into intelligence estimating.

Mr. Carter seems to understand the need to bring the intelligence community under 1) presidential control and 2) legislative oversight. He is working with the Senate Intelligence Committee to frame new legislative charters - statements of mission and authority - for the intelligence agencies. He chose, however, to take up the NSA/NRO question before dealing in public with the proposed charters. The result is that the public sees the tip of an iceberg whose general dimensions are still concealed, and the impression is spread that the President, rather than coming to grips with basic problems of accountability and effectiveness, is simply toying with the organizational boxes.

The remedy is obvious: Put the whole intelligence package - congressional oversight as well as executive-branch management and control - on the table, where it can be inspected and argued out in the round.