Salvadoran officials and Western diplomats say Secretary of State Alexander M. Haig Jr.'s congressional testimony last week may have undermined a politically sensitive investigation here into the killings of four American missionaries.

At the same time, informed Western sources and reportedly even some government officials are concerned that Haig's emphasis on a Soviet "hit list" for Central America and on the military aspects of an ongoing political war here might encourage right-wing elements within the armed forces who advocate the overthrow of the ruling civilian-military junta.

Haig's comments came in testimony last week before the House and Senate committees on foreign relations. Although many Salvadorans agree that the Soviet Union and Cuba have strong interests in Central America, there is a belief, particularly within the civilian sectors of the government, that an emphasis on the Soviets as justification for U.S. involvement here tends to minimize local aspects of the Salvadoran struggle and play into the hands of anticommunist hard-liners.

On Wednesday, Haig told the Senate Foreign Relations Committee that three American nuns and a Catholic lay worker, whose bodies were found in a remote, shallow grave in December two days after they disappeared while driving between the international airport and San Salvador, might have been shot when their van ran a military roadblock.

On Thursday, in response to criticism from the victims' families, Haig backtracked somewhat, saying he had only "laid out" the roadblock scenario "as one of the most prominent theories" in the investigation.

But Salvadoran officials and diplomatic sources close to the investigation said that no such theory is now nor really ever has been considered in the investigation, which has centered on the possible involvement of Salvadoran security forces, and especially on the Treasury Ministry Police, in the murders.

"That [Haig's hypothesis] is a total red herring," said one source. "There has never been the slightest suggestion that that theory is plausible. All four were found shot in the head at close range with Army-type weapons," the source said.

The four women were reported missing Dec. 2, after two went to pick up the other two at the international airport 40 miles from the capital. Their bodies were found buried a considerable distance away from the wreckage of their burned-out van. Salvadoran sources recently said the four had been killed at yet another location and that their bodies were then taken to the gravesite.

President Carter suspended all economic and military aid to the junta and sent a government mission, and later FBI officials, to "clarify" the circumstances of the deaths and what was described as strong circumstantial evidence of military involvement. When leftist guerrillas launched an offensive against the government in January, however, Carter resumed aid on grounds of military necessity and the Reagan administration has sought to separate its own aid program from the ongoing investigation.

Although the women's families and sympathizers in the United States have charged that the investigation has been delayed because it compromises U.S. support of the Salvadoran military, the U.S. and Salvadoran governments have insisted that it is progressing.

One diplomatic source said he feared that Haig's comments were particularly ill-timed, and might be read as a sign that the United States was easing pressure on Salvadoran authorities to pursue the investigation. They come at a time when there are indications of government action on the case, despite continuing risks of alienating sectors of the armed forces.

Salvadoran President Jose Napoleon Duarte has said that fingerprints of Treasury police agents on duty in the area where the women were believed to have been stopped would be sent to the FBI to see if they match prints taken from the van. FBI officials had been waiting for more than two months for those prints.0

After Haig's remarks, Duarte told reporters he was not aware of the secretary's comments, but said that Haig's scenario might be "one possibility. sWe are not overlooking any possibility."

Haig said his theory was based on autopsy reports indicating that glass fragments were found in the wounds of one of the victims, which would indicate that bullets had been fired into the van. But informed sources here said that initial report was later shown to be in error and that there were no glass fragments found in the wounds.

Haig's thesis would also contradict reports that two of the women were raped. Those unconfirmed reports apparently were based on the fact that the undergarments of two of the victims had been removed. When asked about that, Duarte said only that one autopsy report indicated that one of the women was "a virgin." He declined to comment further.

On Haig's outline of a Soviet "hit list" for Central America, with Nicaragua as the first target, El Salvador as the second, followed by Guatemala and Honduras, United Press Nternational yesterday quoted two unnamed top Salvadoran officials as calling that scenario "speculative." Haig, the officials were quoted as saying, "has an incredible imagination."

Sources here said yesterday that the Salvadoran government, while pleased with U.S. military aid is privately concerned that U.S. policy in El Salvador has placed too heavy an emphasis on the military aspects of the conflict and seems to be founded on U.S. relations with the Soviet Union rather than on local Salvadoran concerns.

Government officials here constantly ask for more U.S. economic assistance, saying that the war is a political and economic battle as well as a military one. Western diplomats active here have cautioned that overemphasis on shoring up the Salvadoran armed forces might lead right-wing elements, confident of victory over leftist guerrillas, to try to overthrow the shaky coalition junta.

The salvadoran press also reported that Col. Adolfo Arnoldo Majano, a liberal former member of the junta and one of the leaders of a 1979 coup that brought it to power, has been allowed to leave the country.