The Carter administration's disarray on SALT was revealed over the past three weeks with a backstage interchange between Pentagon brass and the Arms Control and Disarmament Agency (ACDA), beginning in angry disagreement and ending in bureaucratic concealment.

Triggering the episode was ACDA's attempt to reassure Congress that Soviet compliance with the strategic-arms agreement being negotiated in Geneva could be verified - a key issue in the coming fight for Senate ratification. When ACDA claimed the Joint Chiefs of Staff agreed with this dubious assurance, the ballon went up at the Pentagon. Usually tame generals and admirals were so outraged they even put it in writing.

That reflects tension behind the scenes as president Carter continues to promise a new SALT agreement. While not yet ready to go public with their misgivings, the uninformed military are unwilling to blindly rubber-stamp the treaty being negotiated by ACDA Director Paul Warnke. Events of the last three weeks, hinting at deception and subterfuge, could be a foretaste of internal disputes when a new treaty is actually signed.

Verification is a peculiarly sensitive aspect of SALT. While arms-control experts know a verifiable treaty is not necessarily a good treaty, it is one element of the tremendously complicated arms-control puzzle that anybody - including U.S. senators - can grasp. If the Senate is convinced Soviet compliance can be verified, chances for ratification are good.

On Feb. 23, ACDA's paper on SALT II verification was submitted to the Senate Foreign Relations Committee. As revealed in unclassified paragraphs released to the press, verification is far more reliable than experts believe (or than the unreleased classified paragraphs show). "Areas of uncertainty . . . are not such as to permit the Soviets to produce an unanticipated threat to U.S. interests."

What's more, the covering letter signed by Warnke asserted the paper was "approved" by the Joint Chiefs of Staff. That was news to the astonished chiefs when they read about it in The Post Feb, 25. Although the military leaders generally get along by going along, that was too much. Gen. Bernard Rogers, chief of staff of the Army, and Adm. James Holloway, chief of naval operations, were incensed by Warnke's misrepresentation.

The result was a Feb. 28 letter to ACDA Deputy Director Spurgeon Keeny from Vice Adm. Partrick Hannifin, director of the Joint Staff. Even when bracketed by bueraucratic rhetorica, the meaning is clear: "The Joint Chiefs of Staff have not agreed to the [verification] statement." Hannifin said the National Security Council staff was so informed Feb. 22.

"However, we understand that ACDA was not aware of this information" when it sent the letter to Congress Feb. 23, the letter continued. That softening phrase looks suspiciously like bureaucratic hedging. But the letter concludes on a tough note that "we would appreciate your setting the record straight" with the Foreign Relations Committee.

There is reason to believe ACDA had no intention of complying with the request and planned to forget about the letter. But in the usual way of Washington, Hannifin's letter leaked right up to Capitol Hill. Some 10 days later it reached Rep. Robin Beard of Tennessee, a conservative Republican member of the House Armed Serivces Committee. On March 8, Beard wrote the president protesting that "Congress cannot be isolated from hearing dissenting opinions."

Since the matter could no longer be quietly forgotten, it was necessary to give Congress the idea there are "no dissenting opinions." The role fell to the member of the Joint Chiefs most faithful to administration policy: Gen. David Jones, Air Force chief of staff and acting chairman of the chiefs in the absence of traveling Gen. George Brown.

On March 9, two full weeks after Warnke's letter, Jones wrote Secretary of Defense Harold Brown explaining it all: The military helped prepared the report, but the Joint Chiefs "believe it prudent to withhold final judgment on the overall verifiability of any SALT II agreement until all provisions of the treaty are known." The initial anger of the chiefs and Adm. Hannifin's politely accusatory tone had become bland amiability.

Jones' letter was read into the record by Secretary of State Cyrus Vance at a closed session of the Senate Armed Services subcommittee on arms control the next day, March 10. Replying to our question, an ACDA spokesman said Vance's reading of the general's words complied with the original Pentagon request for "setting the record straight" on Warnke's misrepresentation. In short, ACDA plans to neither admit nor concede anything.

But there are still men at the Pentagon, including some four-star officers, who want no part of Warnke's siren song of ensured verification. National security bureaucrats may congratulate themselves about smoothing over the disagreements, but most likely they were only postponing a showdown. The backstage disarray revealed now could erupt into open battle in the months ahead.