Just two days after secret testimony by the new chairman of the Joint Chiefs of Staff reaffirmed the military's opposition to a total nuclear test ban, President Carter ordered U.S. negotiators to press for precisely such a deal with the Soviets.

Carter's propensity for making military decisions against the military's advice has never been clearer. On May 18, at closed-door Senate hearings on his nomination as JCS chairman, Air Force Gen. David Jones unequivocally opposed, in the interests of national security, a "zero yield" ban (prohibiting even low-yield explosions) of all underground tests. He was patently unaware that a "presidential decision memorandum" taking the opposite position was being readied for Carter's signature May 20.

After the fact, the Joint Chiefs met on Blue Monday, May 22, with a majority opposed to the president's decision. The choices before them now are agonizing. Should they loyally back their president to support what they consider a hazardous course for the nation? Should they fully express their misgivings but only in congressional hearing rooms? Or should they go to the nation, either directly or indirectly?

The uniformed military's concern over the test-ban treaty surpasses earlier chagrin over removing troops from Korea, canceling the B1 bomber and suspending neutron-warhead production. Jones, criticized by fellow officers as overly pliable to civilian politicians, made no fuss about such earlier Carter moves as Air Force chief of staff.

Consequently, defense-oriented members of the Senate Armed Services Committee pounded on JCS chairman-designate Jones when his confirmation hearings began May 18. Those senators were particularly concerned about the test-ban treaty. Paul Warnke, chief disarmament negotiator, that week was pressing for a U.S.-Soviet moratorium on all tests prior to negotiations for a "zero yield" treaty.

Answering questions from Sen. Jesse Helms (R-N.C.), the general declared, "I could not recommend a comprehensive test ban . . . in the context of zero testing." The secret transcript reveals Sen. Harry F. Byrd (I-Va.) asking whether Jones agreed that any treaty must permit testing in the 3- to 5-kiloton range, below which tests cannot be verified. "Yes, senator, I do," the general answered.

Sen. Harry M. Jackson (D-Wash.) pointed out that the Joint Chiefs previously opposed a zero-yield treaty. "I subscribe to that," Jones responded. ". . . We don't see any capability to verify the Soviets with any assurance down to zero yield." Pinning Jones down, Jackson asked whether "this is still the JCS position." The response: "Yes, it has not changed."

Jones refused to alter this stance despite prodding by Sen. John Culver (D-Iowa), battering ram of the arms-control bloc. "Isn't it true," asked Culver, that the treaty "will provide us with a fair degree of confidence of compliance and provide a low incentive for Soviet cheating?" The general stood his ground: Cheating "may not be quite that difficult . . . I am not assured that we would have confidence the Soviets couldn't cheat."

Culver persisted, suggesting that a treaty lasting five years or less would not threaten reliability of the U.S. nuclear stockpile. Jones replied that "something unexpected" can always effect "reliability," adding, "You just may not find the problems if you don't do testing."

Jones clearly was uninformed about other plays elsewhere in the Washington arms game. Warnke that week failed to get his pre-negotiations moratorium but won agreement on a zero-yield, five-year treaty (three years longer than the chiefs prefer). The "presidential decision memorandum" signed May 20 directed negotiators to start from Soviet proposals for on-site inspection and unmanned seismic-detector stations - considered inadequate for verification by Pentagon scientific experts.

The JCS convened May 22 to talk it over. Army Gen. Bernard Rogers, Adm. James L. Holloway and Marine Corps Gen. Louis Wilson were dead against it. The new Air Force chief of staff, Gen. Lew Allen, wavered. Jones seemed to back away from his strong stance, suggesting that the chiefs should study the question a little more.

But during his confirmation hearings, Jones had locked himself into independence. When one defense-oriented senator after another asked whether he would be his onw man as JCS chairman, Jones replied time and again: He would not travel the country making speeches, but he would give Congress his own blunt opinion even if it conflicted with Jimmy Carter's.

The president and the general obviously conflict on the test-ban treaty, barring an instant conversion by the general. Jones has told friends he will be an "activist" chairman, but it is not clear whether he means activity in behalf of administration policies or activity in behalf of the military's position. The answer will come from his next step on the test-ban treaty.