High-level conflict over the routine administration decision to postpone or attend a March 25 SALT session in Geneva with the Soviet Union reveals a troubling weakness in President Reagan's national security apparatus, threatening more serious problems in the future.

The issue seemed simple enough when on Feb. 20 Richard V. Allen wrote a brief "Dear Cap" note to Secretary of Defense Caspar Weinberger. Reagan's national security assistant instructed Weinberger to set up a meeting with the State Department, the Central Intelligence Agency and the Arms Control and Disarmament Agency. Subject: the March 25 Geneva compliance-review meeting of the Standing Consultive Commission (SCC).

Allen quickly found himself in a bureaucratic cross fire so lethal that, three weeks later, the fast-closing question of the March 25 meeting was still unresolved and Weinberger never has called the meeting Allen asked for. The leaves this question: In his effort to avoid the open warfare that so weakened the Carter administration's State Department and National Security Council staff, is Reagan substituting an even more costly clandestine warfare?

Allen's memorandum to Weinberger was never acknowledged by Weinberger. Instead, nearly one week later Secretary of State Alexander Haig's deputy, William P. Clark, and Weinberger's deputy, Frank Carlucci, sent word back to Allen that a "joint position" was being developed and that "if this matter requires" the president's attention, the president (not Allen) would be informed.

Having effectively rejected Allen's instruction to Weinberger, the anti-NSC bureaucracy then called a meeting on its own on March 4, chaired not be defense, as Allen wanted, but by the State Department. The department is in the forefront of those wanting to postpone the March 25 session.

This high-level meeting was convened by Rick Burt, director of the department's political-military bureau. Clearly under instructions, Burt blithely revealed that Haig and Weinberger at breakfast that morning had agreed to postpone the March 25 Geneva session for two months to give the United States time to get its nuclear policy in shape.

Among those gathered around the table in Burt's State Department conference room was Maj. Gen. Robert L. Schweitzer, the NSC director of defense policy and Allen's agent. He refused to accept the Haig-Weinberger verdict, just as top officials at ACDA had refused to accept a proposed State Department cable to the U.S. Embassy in Moscow on Feb. 27 announcing postponement of the Geneva meeting. In vetoing the postponement notice, Acting ACDA Director Michael Pillsbury insisted the decision could not be made by Haig and Weinberger alone but required "government-wide" participation -- meaning Allen and the NSC.

The Joint Chiefs of Staff also opposed postponement of the Geneva session and refused to go along with the State Department's Feb. 27 cable, despite Weinberger's consent. The chiefs want to hear what the Russians have to say about their "compliance" with provisions of the treaties.

In addition to this tactical reason the uniformed Pentagon leaders give for opposing any postponement, some high officials -- particularly in that one-time nest of dovishness at ACDA -- want to use the March 25 meeting to unveil nearly 40 alleged Soviet violations of the pacts. These are contained in a 167-page supersecret document ("the hottest document in town," one official told us) that has been painfully and scrupulously assembled by ACDA. It could put Moscow on the defensive on the compliance issue.

Haig, Weinberger and their aides privately agree that this compilation of alleged violations could become a highly useful U.S. tool in the future. To table it at the March 25 meeting, however, would be premature, they say; charging Soviet violations of SALT I (expired) and Salt II (never ratified) might tend to reduce U.S. flexibility if President Reagan decides not to abide by the unenforceable treaties in the future (as Haig has announced the United States will do for the present).

Some hard-liners, said by aides to include NSC staff chief Dick Allen, believe postponement of the March 25 meeting will cost the United States a choice time to play this trump card. Other hard-liners disagree; the alleged violations should not be thrown at the Russians before Reagan knows exactly how he wants to play the SALT game.

Accordingly, conflict over postponing the Geneva meeting cannot be blamed on ideology. It is the result of a national security process without form or substance, so vulnerable that it makes for more baleful jokes than it produces tough decisions