Last September veteran diplomat Morton I. Abramowitz was offered the choice post of assistant secretary of state for East Asian and Pacific affairs, the top Asian policy job in the government. He was naturally pleased--but he had enemies who were not.

Partly because of their political and bureaucratic opposition, his appointment did not develop, and he was selected instead in early October to be U.S. ambassador to Indonesia. President Reagan himself telephoned the offer; Abramowitz accepted.

But within a few weeks, disappointing word was mysteriously received from Jakarta that the Indonesian government preferred that he not be named.

A statement issued yesterday in the name of Secretary of State Alexander M. Haig Jr. announced with regret that Indonesia will not accept this "truly outstanding Foreign Service officer," thus ringing down the curtain on six months of agonizing uncertainty for Abramowitz, and quite possibly presaging the end of a 22-year diplomatic career.

What happened to Morton Abramowitz is an extraordinary episode, even for unusual times, illuminating a netherworld of intrigue that has affected several Reagan diplomatic nominations, as well as the torturous pace at which a number of key personnel decisions have been made.

Though he was backed by Haig and at times personally approved by Reagan, Abramowitz was opposed not by outsiders but by enemies within the administration itself.

Among their most important weapons in this effort was an anonymous and confidential paper, much of it inaccurate, which was prepared by military officers, reportedly with the help of Abramowitz's former CIA station chief at a post abroad, in an effort to stop Abramowitz's rise within the administration.

After Reagan and his senior assistants decided to nominate Abramowitz as ambassador to Indonesia, the internal paper mysteriously found its way to the top rank of the Indonesian government and ultimately into the hands of columnist Jack Anderson.

The document apparently played a role in Jakarta's decision, conveyed in preliminary terms last November and in final terms two weeks ago, not to accept Abramowitz as U.S. ambassador.

Another shadowy aspect of the case, prominent in reporters' questions about it at the State Department yesterday, is "the religion angle." Abramowitz is Jewish, and Indonesia is a predominately Islamic country. Despite rumors that this affected Jakarta's decision, both State Department spokesman Dean Fischer and Abramowitz himself, in a terse statement yesterday, said the Indonesians never conveyed an indication that religion was a factor.

Abramowitz, 49, has amassed one of the most outstanding records in the active U.S. diplomatic service, most of it involved with Asia. Among other things, he served in Taiwan and Hong Kong, as political adviser to the chief of the U.S. forces in the Pacific, as the Pentagon's senior specialist on Asian affairs and, in the three years preceding his travail, as U.S. ambassador to Thailand.

Both in the Pentagon and as ambassador to Thailand, Abramowitz received awards for unusually effective service, including the prestigious Joseph C. Wilson Award for achievement in diplomatic affairs, and last year the President's Award for Distinguished Federal Service. At the same time, though, his blunt manner and some of his bureaucratic moves and positions earned him the enmity of some officials.

Abramowitz was considered especially vulnerable in connection with Reagan administration posts because of a long friendship with Richard C. Holbrooke, the Carter administration's assistant secretary of state for Asian affairs, who is anathema to many conservatives. The two men, though friends, did not always agree, and Abramowitz had many admirers who disliked Holbrooke.

Abramowitz remained in Bangkok for seven months after the onset of the Reagan administration. When he was replaced in that post last August the word was around that he was likely to be nominated as ambassador to the Philippines, in part because President Ferdinand Marcos is said to have personally expressed his admiration for Abramowitz and his interest in his appointment.

In mid-September, back in Washington, Haig had decided to replace his assistant secretary for Asian affairs, John H. Holdridge, and to offer him the embassy in the Philippines. It was Haig's idea, according to several knowledgeable sources, that Abramowitz would move to the top Asian affairs job, where his combination of experience and bureaucratic toughness was high on Haig's qualifications list.

After Abramowitz was offered and accepted the job in conversations with an aide to Haig, the story leaked to conservative circles in Washington and to the press, setting off alarms from longstanding enemies as well as some Republicans who considered him too close to the Democrats.

An unsigned Oct. 1 paper headed "Point Paper on Morton Abramowitz" was one result of this alarm. Stamped "confidential," it described Abramowitz as a person whose "political philosophy is akin to McGovern, Muskie and Mondale" and whose wife had been a staff aide of Muskie, McGovern and Carter.

In fact, Abramowitz is considered by most who know him to be a tough-minded conservative in international affairs. His wife, Sheppie, worked for about a year as an aide to then-Sen. Edmund S. Muskie in 1970, but reportedly did not work for the other two.

The document also described Abramowitz as "the architect" of U.S. troop withdrawal from South Korea, a course he publicly and privately opposed until President Carter adopted it as a policy of his administration. It also claimed, erroneously, that Abramowitz "worked very hard" to provide diplomatic recognition and "a massive foreign aid program" to Vietnam.

The authorship of the memorandum has not been definitely established. A senior administration official familiar with it said: "As best we knew, it came out of Defense, not out of the White House," and that this impression had subsequently been confirmed by high-level State Department inquiries.

It is widely reported in policy circles that one of the most prominent opponents of Abramowitz's elevation was retired Gen. Richard G. Stilwell, once U.S. military commander in South Korea, later a transition and National Security Council consultant to the Reagan team and currently deputy undersecretary of defense for policy. Stilwell is currently in South Korea, and sent word through an aide yesterday that he had "nothing to do with" the opposition to Abramowitz.

Another person widely reported to be involved is Daniel C. Arnold, who was CIA station chief in Bangkok for about a year during Abramowitz's tenure as ambassador. Arnold is considered very close to Gen. Chamanan Kriangsak, who was ousted as Thai prime minister in February, 1980, while Abramowitz was U.S. ambassador and reportedly felt lack of U.S. support was part of the cause.

Arnold said yesterday that he and Abramowitz had "no problem" when they worked together, but that they quarreled in late 1980 over his return to Bangkok as a private consultant after retiring from the CIA. Last November, Arnold registered with the Department of Justice as a paid agent of the Thai government with a $50,000 initial retainer.

A friend of both men, who asked not to be named, said Arnold had told him last fall that "we are getting up a memo" to stop Abramowitz, and that it was being sent in a hurry to the White House. Arnold denied helping to draft such a memo, but said he did help to "check out" questions about Abramowitz on request from unnamed friends.

A third person, who acknowledged that he opposed Abramowitz for the top Asian job, is Ray Cline of the Center for Strategic and International Studies at Georgetown University. But he said he knew nothing of an opposition memo.

In the face of opposition to Abramowitz and a threat by Holdridge to resign rather than go to Manila, Haig dropped his plan for this switch. However, questions had been raised at the White House about Abramowitz in the process, particularly for the post in the Philippines where there are large U.S. military bases and military interests.

A White House personnel official is credited by insiders with suggesting that Michael H. Armacost, who was preparing to go to Indonesia but who had good relations with the U.S. military, be sent to Manila, and that Abramowitz be sent to Indonesia. Apparently there was no consideration of the potential problem of sending a Jewish ambassador to an Islamic country.

In the first week of October, the switch was decided. Reagan, despite the "point paper" against Abramowitz and a White House document incorporating some of it, approved the appointment to Jakarta and late that month formally asked Abramowitz, by telephone, to take the job.

Indonesians were at first puzzled and then unhappy at the switch. In November the retiring U.S. ambassador, Edward E. Masters, was told by a high Indonesian official that the country's leader, President Suharto, preferred that Abramowitz not be sent. Later it was reported that Suharto had been given a copy of an anti-Abramowitz paper believed to be a White House document.

Top U.S. officials waited until January before taking direct steps--a letter and telephone call from Haig to Indonesian Foreign Minister K. Mochtar. However, the Indonesian responded that "the well has been poisoned" and Abramowitz could not be accepted.

Besides mention of the paper, Indonesians have given no clear reason for their attitude. Reports that reached the State Department and Capitol Hill suggested that the Indonesians, among other objections, were concerned by advice from someone in Thailand that Abramowitz "might try to run your country." There is also an unconfirmed report, heard by a well-informed private citizen, that "the Jewish angle" came up in conversation with the Thais.

Hoping that the objections would clear up, and encouraged by some hints to that effect, Haig waited until April to propose Abramowitz formally to Jakarta as U.S. ambassador. Though Haig sent the formal proposal with what is described as an unusually strong endorsement, the Indonesians replied early this month that they would not accept.

Haig's statement yesterday regretted this action and praised Abramowitz. "There has never been any question in the president's mind or my own that he was an excellent choice for the post in Jakarta," the statement said.

After reading the statement, spokesman Fischer added: "What we are faced with now is an examination of the possibility of another suitable assignment for Ambassador Abramowitz." However, no new job is in sight for the diplomat who was vaulted toward the top, only to fall from the arrows of unseen opponents.