Secretary of Defense Harold Brown warned yesterday that removing Gen. David C. Jones as chairman of the Joint Chiefs of Staff before the expiration of his term would be an "unprecedented act" that "would send a signal to military officers that loyalty to civilian authority is not what is rewarded."

Press reports emanating from Republican quarters have suggested that President-elect Ronald Reagan will, one way or another, remove the Air Force general from his job soon after the inauguration.

The report that Jones might be fired or, more gracefully, asked to step down has generated considerable controversy in both political and military circles because it goes well beyond Jones himself to the substantive issues of civilian control over the military, the role of the joint chiefs and the confidence of a president in the military advice he receives.

"There is no question," Brown said in a telephone interview yesterday, "that the president has the right to fire, or ask for the resignation of, the chairman of the joint chiefs . . . though it has never been done. What concerns me here is that what may be at issue is a discharge for loyalty to civilian authority, for living by the rules. If that's done, it would be sending the wrong message to all military officers . . . that they have to anticipate the future political point of view and be loyal to that rather than subordinate to civilian superiors.

"The role of the senior military has to be understood. Their function is to give advice and argue things from the military point of view," the outgoing defense secretary continued. "Jones was very forceful. He was in favor of the B1 bomber when he was Air Force chief of staff." But when civilian authorities later made a decision against that bomber, Brown said, Jones, as senior officer, could either support that decision, which meant not undermining it, or could resign.

Jones wound up supporting the decision to scrap the bomber and that is high on the list of reasons a number of well-placed conservative Republicans want him out. Jones has some enemies among top military officers as well because he also lent support to the administration's position in the strategic arms limitation talks with Moscow and on the Panama Canal treaties.

The paradox of the debate is that Jones' enemies want him out because they feel he has politicized the office by being a predictable rubber stamp at a time of serious misgivings about American military power, while those who believe Jones should finish his term warn that his ouster would indelibly politicize the nation's top military job. Jones also has many supporters who argue that he has played a skillful behind-the-scenes role as an advocate for the military.

Brown is the second secretary of defense who has sharply warned against prematurely ousting Jones. James R. Schlesinger, who ran the Pentagon in the Nixon-Ford administrations, also has warned against punishing military officers for the policies of their civilian superiors and against tampering with the constitutional principle that the military must remain apolitical.

Carter reappointed Jones last June for a second two-year term, which means he normally would have another 18 months to serve as the nation's top military officer.

Brown was also asked earlier yesterday in an interview on "Face the Nation" (CBS, WDVM) for his reaction to the reports about Jones. Brown pointed out that nothing has actually happened yet, but he reminded the incoming administration that the nominee for secretary of state, Alexander M. Haig Jr., was kept in his former military post by the Carter administration despite political controversy.

When he took over in January 1977, Brown said, two top officers "were subject to considerable criticism."

One was the former chairman of the joint chiefs, the late Gen. George S. Brown, who had been accused of bias because of some public remarks he made about the influence of Jews. The other was Haig, who had been "attacked on the basis of his previous service in the White House and political activity." Haig was serving as supreme allied commander in Europe when the Carter administration took office.

Brown said that, in both cases, the administration took a couple of months to study the situation and "concluded that both of those people were doing a good job where they were and we decided we should leave them there and that to do otherwise would have been to politicize those military offices, which I think would have been a great disservice. Anyone who would easily dismiss someone on the basis of political factors I think would be politicizing the military."

Reagan's press spokesman, James Brady, has said publicly that "I know Ronald Reagan has made no decision regarding Gen. Jones." Privately, senior transition officials also say that no recommendation to fire Jones has gone to Reagan and that Harold Brown's description of how the cases of George Brown and Haig were examined by the Carter administration over a couple of months may describe the process Reagan will follow. One source said that, to preserve some continuity in the top jobs, it would not be wise to oust the chairman at the same time a new defense secretary was taking over.

There is no doubt that Jones has some enemies in powerful places who want him out for what are viewed as sound military reasons or for political vengeance, officials on both sides agree.But there is no certainty that he actually will be asked to resign, transition sources say. Jones has said, through a spokesman, that while he serves at the pleasure of the president, he intends to finish his term and will not resign voluntarily.

The initial story in The Washington Star alleging that Reagan "plans to dump" Jones and that the Reagan transition team at the Pentagon had already recommended it to the president-elect may have taken away whatever freedom of action the incoming administration wanted on this issue, officials on both sides say. It would be difficult now to arrange any graceful departure for Jones if the president decided he didn't want to keep him. But if Reagan decides to let Jones finish his term, it may look as if he gave in to the general's backers.