The murder last week of Philippines opposition leader Benigno Aquino Jr. has caused deep concern in the Reagan administration about its hopes for future stability and a return to democracy in a country bound to the United States by strong emotional ties and vital strategic interests.

It was this concern, U.S. officials acknowledged privately, that prompted the administration to start staking out a position where it can disassociate itself from the government of President Ferdinand Marcos if the evidence links him or his associates to Aquino's assassination.

Throughout the week, administration officials sought to draw a distinction between U.S. ties to Marcos and the long-term relations between the American and Filipino peoples.

The United States, the officials made clear, has a major stake in ensuring that its rights to naval and air bases in the Philippines are safeguarded and in helping the strategically situated Southeast Asia nation avoid internal strife that might bring it under anti-American, leftist control.

And they left no doubt that if achieving those goals requires it, Washington is prepared to jettison the favored status it has extended to Marcos for 18 years.

That would be a quantum shift for the Reagan administration, which has given the Marcos relationship a new warmth and special attention. The serious consideration being given such a step underscores the U.S. belief that Aquino's murder could jolt the status quo imposed by Marcos on Philippines politics over the past two decades and turn the country in uncertain new directions.

So far, the officials stressed, there is no evidence linking Marcos or anyone else to the shooting last Sunday at the Manila airport, where Aquino arrived after a three-year absence in the United States. But, as one administration official noted:

"The circumstances were such that it looks awful for Marcos and his government. There is a strong automatic assumption that it couldn't have happened without some kind of official connivance. So the burden is on the Philippines government to prove its innocence, and anything that smacks of a whitewash will only make the situation worse."

The administration has adopted a wait-and-see attitude on whether the Marcos government can mount a credible probe that will exonerate it from the suspicions of complicity. But many U.S. officials, while conceding that they don't know what happened or why, privately are pessimistic.

They point out that the killing violated all the unspoken understandings and "rules of the game" that were commonly assumed to govern the relations between Marcos and the best known and most charismatic of his opponents. Marcos, they note, could get away with using his dictatorial powers to imprison or exile Aquino, but the fear of internal repercussions and the anger of the United States were regarded as effective barriers to assassinating someone of Aquino's stature.

"Whatever else can be said about Marcos, he's not stupid," one official said. "He knew what the consequences would be, and it seems inconceivable that he would have ordered or sanctioned the murder. And even though Aquino talked a lot about the possibility of martyrdom, it's hard to believe that he really expected to be killed."

Still, officials with knowledge of Philippines affairs give no credence to suggestions that the murder was the work of communists or of rivals for the opposition leadership. Instead, they believe that the killing couldn't have happened without some involvement by the authorities.

No one will say so openly, but widespread suspicion is known to exist within the administration that the assassination was the work of forces within the Filipino military and security apparatus that acted without Marcos' knowledge.

Fueling that suspicion have been reports that Marcos' wife, Imelda, met with Aquino in New York in May to urge him not to return and warn that he had been marked for death by allies of her husband who were out of control.

All this has reinforced an impression, widespread among Philippines experts for some time, that Marcos, 65 and plagued by poor health, has started to lose his tight grip and that, as his power has deteriorated, the military and political factions allied with him are beginning a struggle for supremacy.

Such a struggle will have important implications for U.S. interests. Most directly at issue are continued U.S. rights at Clark Air Force Base and the Subic Bay military complex, the largest American military installations outside the United States. In June, the two countries renewed an agreement on the bases that will pay the Philippines $900 million over the next five years.

U.S. military officials regard these bases as essential for projecting American military power into both the northern Pacific and the Indian Ocean. The latter has become especially important because the U.S. rapid-deployment strategy envisions the Indian Ocean as a prime route for ships, planes and men to deal with potential military emergencies in the Persian Gulf with its vital oil supplies.

The U.S.-Philippines relationship also bears a strong emotional component from the period between 1898 and World War II, when the Philippines were the laboratory for America's principal experiment with colonialism. In both countries, the years of American tutelage and the shared bloodshed of the wartime struggle to free the Philippines from Japanese occupation are widely regarded as having forged a special and unbreakable bond.

In fact, during the decade when Marcos used dictatorial emergency powers to stifle dissent, the million-member Filipino community in the United States, supported by American human-rights activists, became the principal center of opposition to his government.

Coincidental with the murder of Aquino, the administration was embarrassed last week by the leaking of secret government documents indicating that U.S. intelligence agencies may have turned a blind eye on efforts by Marcos agents to spy on and harass Filipinos in this country.

In the main, however, dissident expatriates like Aquino found the United States a safe haven from which to attack the government at home and criticize U.S. officials for their coziness with Marcos. When Marcos visited here last fall, he expressed dismay that the U.S. government permitted Aquino and others to carry on their activities so visibly.

Indeed, Washington has tried throughout the Marcos era to balance its Manila dealings with its sense of a special tie to the Filipino people.

In the Carter administration, with its emphasis on an activist human-rights policy, there was some effort to loosen the identification with Marcos by reducing the normally high American profile in the Philippines.

But that approach was more stylistic than substantive. When Carter's secretary of state, Cyrus R. Vance, was asked by a congressional committee how he could justify large-scale military aid to a government with such a poor human-rights record, he candidly replied that the American bases were so important that they had to take precedence.

Under Reagan, who severely criticized Carter's rights policies as meddling in the affairs of friendly countries, the approach has been markedly different. The present administration has embraced Marcos warmly as a dependable ally and foe of communism. It sent Vice President Bush to Manila, where he praised Marcos in enthusiastic terms, and last fall it was host to the state visit by the Filipino leader.

However, administration officials insist that they also had been applying Reagan's advocacy of "quiet diplomacy" in human rights. The officials say that the administration, aware that the Marcos era was drawing toward an end, had been urging him quietly to prepare his country for a return to democratic government.

For that reason, Aquino's murder was especially dismaying to the administration. He was regarded as a moderate who balked at violent resistance to Marcos and who advocated continued close ties with the United States.

That caused the administration to view him as a potentially important transitional figure who might have played a major role in reconciling the feuding political factions and inducing them to cooperate with the government. He also was seen as the opposition figure with the best chance of becoming president either in the immediate Marcos aftermath or, more likely, at some future stage when genuinely free elections become possible.

From the U.S. point of view, his death was a double-edged blow. It could make him a symbol of martyrdom that will fan domestic discontent and accelerate the deterioration of Marcos' power; and it could leave a leadership void within the opposition that will be filled by someone of more extreme views.

For the moment, the administration is sitting tight and watching whether Marcos will be able to disperse the fallout from the assassination in a way that will restore his credibility and ward off violent internal reactions.

The administration is not planning any immediate drastic moves like cutting off aid unless, as one official put it, "the smoking gun is found on Marcos' desk." On Friday the White House said that, despite calls for Reagan to drop the Philippines from his five-nation Asian tour this fall, the president has no plans to skip his scheduled stop in Manila.

Still, that position could change, as was made clear last week when administration officials went out of their way to stress that U.S. relations with the Philippines have a special enduring quality that transcends the Marcos government.

If it becomes apparent that Marcos is unable to extricate himself from blame in Aquino's murder, the administration seems to be positioning itself to join a chorus of condemnation and take whatever steps it considers necessary to preserve American interests in the Philippines.