During the first week of June, Secretary of Energy James Schlesinger hand-carried a top-secret letter to President Carter's office that for the first time injected him squarely into the turmoil over arms control and national security within the administration.

Schlesinger's letter to the president aligned him with the Joint Chiefs of Staff (JCS) against the proposed five-year "zero yield" nuclear test ban treaty - a ban on all underground explosions, including the 150-kiloton tests now permitted. As head of the department assigned the duty of certifying the nation's nuclear arsenal, Schlesinger warned Carter that nuclear testing is essential to maintain warhead reliability. If asked or directed to testify before Congress, he would say just that.

That gave the military a badly needed Cabinet-level civilian to help slow the rush to a total test ban. In a broader sense, it reintroduced a seasoned bureaucratic disputant into the debate over how many national-security risks can be taken for the sake of arms control.

Schlesinger's courageous though indiscreet advocacy of higher arms spending in 1975 ended with President Ford firing him as secretary of defense. Schlesinger is the only Republican in the Carter Cabinet, and discretion has been his watchword. He says nothing publicly about national security, and nobody has ever heard him utter one critical word, on or off the record, about Jimmy Carter (in contrast to his sometimes pungent off-duty remarks about Richard Nixon and Gerald Ford when he was a Cabinet member for them).

But in fact Schlesinger has been distressed by national security policy, particularly by Chief Disarmament Negotiator Paul Warnke's operations. Schlesinger is perceived by some defense-oriented Democrats in Congress as Carter's ultimate salvation, whom he eventually will call upon to pick up the pieces. But to do that, Schlesinger must establish a record of having warned the president that present policies lead to disaster.

How can that be done unless Schlesinger throws discretion to the winds and trespasses directly into national security? The answer is that the legal jurisdiction of his new Department of Energy includes the nuclear-testing laboratories formerly under the old Atomic Energy Commission; Schlesinger has the duty of certifying the reliability of the national stockpile.

Schlesinger's experts at the Energy Department began early to obstruct Warnke's push for quick negotiation of a zero-yield test-ban treaty. With atmospheric tests barred by the 1963 treaty and underground tests limited to 150 kilotons by the 1974 treaty, the national laboratories say it is already difficult to certify reliability of the stockpile; with no testing it will be impossible. As for the Soviets, only continual on-site inspection could verify compliance with a zero-yield ban, and Moscow flatly rejects it.

Such misgivings by both Department of Energy and JCS experts led to their exclusion from hush-hush Anglo-American talks here in mid-April. Nor were they consulted before Carter signed presidential decision memorandum 38 on May 20, calling for a five-year "comprehensive" (presumably zero-yield) treaty with the Russians.

Schlesinger concluded that certain high officials - Warnke and to a lesser degree Secretary of State Cyrus Vance - had forced that process too quickly. He felt it was time a high civilian official gave the Joint Chiefs some help. (While privately voicing reservations about a five-year zero-yield pact, Secretary of Defense Harold Brown has made no pitch against it.)

Thus, Schlesinger decided to handcarry his letter to the president. Its distribution was limited, with copies outside the Energy Department going only to Brown and National Security Adviser Zbigniew Brzezinski. However, Schlesinger wanted publicly to disclose his views; he was prepared to do so a few days later on "Meet the Press," but the question was not asked.

With the president repeatedly on record for banning all nuclear tests (that is, zero-yield) and having signed PDM-38 nearly a month ago, the debate would seem to be over. But few decisions are ever final in the Carter administration, particularly when the persuasive Schlesinger makes a serious move.

With both the Joint Chiefs and Schlesinger now on record against a zero-yield test ban, a potent threat has been raised to the grand strategy of the arms-control lobby: to push a test-ban treaty ahead of SALT II on grounds it would be harder to oppose and would improve the climate for the broader treaty.

Jim Schlesinger's re-entry into national security affairs transcends the test-ban treaty. For 16 months some national security policymakers have been congratulating themselves that Schlesinger's intellect and combativeness were safely harnessed to the daily drudgery of natural-gas pricing. Now that he has stepped out of that harness, congratulations of a different sort may be in order.