A special diplomatic mission led by Assistant Secretary for Inter-American Affairs William Bowdler and William D. Rogers, who held the same position under presidents Ford and Nixon, arrived here today to investigate charges that Salvadoran government security forces may have been involved in last Tuesday's murder of four American missionary women.

The investigation marks the first time since the Carter administration began backing the government junta that it is addressing publicly the charges of government forces involvement in terrorism here.

Bowdler and Rogers are to report next week to President Carter on the American deaths -- three nuns and a lay worker who were shot, physically abused and buried south of the capital.

Yesterday, the State Department suspended aid following the announcement by U.S. Ambassador Robert White that military and local officials in the area where the bodies were found buried them without identification a full day before church representatives and White himself were informed of the discovery of the grave.

The government, before and after the official "discovery," has denied any official involvement in the murders.

No matter what the outcome of the Bowdler-Rogers inquiry, however, the problem of what church leaders here call "savagery" among the Salvadoran armed forces will remain.

The alleged complicity of members of the Salvadoran military in numerous incidents of torture and murder has undermined all attempts at social and economic reforms in this country, served to polarize the nation and had no discernible lasting impact on leftist guerrilla movements. It may even bolster the rebels by forcing recruits into their ranks.

The problem of military terrorism has brought about the disintegration of two civilian-military coalitions since the junta took over following a coup last year and has split the once-strong Christian Democratic Party that officially remains part of the government.

The wanton violence now appears on the verge of splitting the military itself. One Army officer who has supported liberal junta member Col. Adolfo Majano said this week that in conversations with like-minded colleagues -- currently a minority of several dozen young officers -- there is growing concensus that they should leave the military. Several are considering joining the opposition, this officer said.

The right-wing terrorism operates even within the armed forces. Several officers have received threats branding them as "communists." Majano survived an assassination attempt and just returned to the contry tonight after spending l l/2 weeks in Panama for security reasons.

Yet until the American women were abducted, at least two of them raped, all of them tortured and finally shot, the State Department and moderate civilians in the government here played down and often tried to obscure the problems within the military.

When eyewitnesses have said uninformed government troops committed murders, it has been officially suggested that the uniforms were stolen ones worn by the guerrillas. When particularly prominent people have been killed, such as San Salvador archbishop Oscar Romero last March, it has been suggested that the left did it so that the right, or the government, would be blamed.

In no case has it been proved that the left killed someone and attempted to blame it on the right.

Blame for many murders here is hard to assess since some are apparently common crimes disguised as political ones. But church and human rights investigators who have sifted through the available information attribute most of the 9,000 apparent political killings this year either to the government's soldiers or paramilitary groups repeatedly alleged to work with them.

The U.S. Embassy, members of the five-man governing junta and the minister of defense, meanwhile, have all conceded on numerous occasions that some soldiers are guilty of "abuses." For months these officials have made public denunciations and declarations about implementing a "process of control" over the renegade elements of the armed forces. There are now as many abuses being reported as ever.

Although the moderates in the government have established their powerlessness to control terror, their moderate opponents, including high-ranking church officials, say they do not believe the Christian Democrats and the more liberal soldiers who have remained in the regime are ordering the killings. What the church officials object to is that those moderates continue to lend their names to the government.

When a group of young Army officers overthrew the corrupt regime of general Carlos Humberto Romero in a bloodless coup last year, their only real constituency was their troops and a U.S. government hoping to find some moderate alternative to a radical leftist takeover.

Through long history, most of the former Spanish dominions in the New World have regarded the military as the final arbiter of a nation's future. Often the army was the only smoothly functioning institution in the country.

While Americans tend to think all military coups are rightist, both Peru and Panama offer examples of liberal soldiers seizing power. The young officers of El Salvador expected to follow in that liberal pattern, ousting the oligarchy and establishing sweeping reforms.

At first their takeover disoriented the left, and when socialists and even communists were brought into the first coalition government, a kind of peace seemed to have been won.

It lasted for less than three months. The key to the coup's support among the majority of troops was not advocacy of reforms but a promise to fight communists and most importantly to "maintain the integrity of the armed forces." That would be done by ridding the country of corrupt generals. Reforms would be a secondary matter.

After decades of ruthlessly eliminating any opposition to the ruling class, the Army and especially its allied security forces -- the National Guard, national police, treasury police and a paramilitary network of tens of thousands of vigilantes -- had established a long record of brutality.

The only way for the new regime to cleanse the military ranks as civilian reformists demanded would have been massive discharges. Only a few officers were expelled, many of them because they had failed to join in the coup. The troops decided to back their commanders rather than the civilians criticizing them.

The first coalition collapsed. Government repression continued. Guerillas renewed their activities and this year's bloodbath began. When the Christian Democratic Party decided to participate in a new coalition 11 months ago, its members believed they understood the mistakes of their predecessors.

Party leader Napoleon Duarte was himself a victim of past military abuses.

He was forced into exile after the armed forces annulled an election he won. Once in the government, he sought to avoid open confrontation with the military at almost any cost.

At a press conference Thursday night, Duarte said that at least 300 members of the National Guard have been dismissed since he entered the government. He knows of nine members of the guard and five national police who have gone to jail for "abuses", he said.

Asked why this information had never before been publicized in order to send a message to the troops, Duarte said, "What we cannot do is we cannot make propaganda out of this." To do so, he suggested, would upset everything.