The Reagan administration, seeking to dispel the impression that it is indifferent to democracy and human rights in El Salvador, asserted yesterday that its emphasis on combatting the leftist guerrillas in that country does not mean it has stopped supporting reform there.

In a lengthy effort to explain the administration's position, State Department spokesman William Dyess said first priority is being given to helping El Salvador's ruling civilian-military coalition fight "the terrorist insurgency of the left because it is so extensively supported from the outside, by Cuba and other countries."

But he also said, "We support their democratic change, individual rights and economic progress, but terrorism is the enemy of all of these objectives. And I speak now of terrorism from the rights as well as from the left."

State Department sources said the statement was prompted by the fact that administration pronouncements on El Salvador in recent days have focused almost exclusively on the leftist guerrilla insurgency and have given short shrift to allegations that the rightist forces in the civil war there have been responsible for thousands of murders and human rights violations.

On Tuesday, for example, Dyess said unequivocally that the United States considered it so urgent to check the leftist threat that U.S. aid was no longer being linked to conditions set last month by the Carter administration -- namely that the Salvadoran government continue making reforms and investigate thoroughly the murder, allegedly by rightists, of four American Roman Catholic missionary women.

According to the sources, the administration was worried lest these movies, which have been reported extensively in the press, were creating the impression that the United States, in the name of fighting communism, has turned its back on humanitarian principles and given an uncritical embrace to what many critics contend is an authoritarian regime.

El Salvador's governing coalition, which came to power following a 1979 military coup, claims it is committed to reform and a centrist position between the country's feuding factions of the extreme right and left. But it has been subject to repeated charges, in some cases from congressional liberals and prominent Roman Catholic clerics in this country, that it actually is a captive of the right or has been unable to control excesses by elements in the Salvadoran security forces sympathetic to the right.

That the Reagan administration's move toward increased support of the Salvadoran regime is causing uneasiness even among some of its supporters was made clear Tuesday by Sen. Charles H. Percy (R-Ill.), chairman of the Senate Foreign Relations Committee.

Although he endorsed the administration's approach after conferring with Secretary of State Alexander M. Haig Jr., Percy said he had told Haig "clearly" that aid must be coupled to a thorough investigation of the missionaries' murders. Percy also said he had reminded Haig of the Vietnam war lesson that "you could not move without the support and cooperation of the American people."

In a related development, reliable sources said yesterday that Lawrence Pezzullo, a career Foreign Service officer who had been the Carter administration's ambassador in Nicaragua, will be kept in that post. Pezzullo has been leading U.S. efforts to halt the flow of arms through Nicaragua to the leftists in neighboring El Salvador.