U.S. Ambassador Deane R. Hinton said last night that the Reagan administration "should" and "will" certify El Salvador's government as eligible for more than $200 million in U.S. military and economic aid this year.

U.S. officials here said this morning that the certification, due by law within the next week, would be issued Friday in Washington.

The president is required to certify to Congress twice a year that the government it backs here is making progress in human rights, social and economic reforms and the prosecutions of Salvadoran soldiers who allegedly murdered U.S. citizens. Only "very strong" evidence to the contrary could prevent the certification from being made, Hinton said in an interview. The alternative, he said, would be a probable defeat for the Salvadoran government in its war with leftist-led insurgents.

"Surely," Hinton said, "any president or any administration that thinks it would be a disaster if this country was taken over by a totalitarian Marxist regime is going to hesitate a long time and the evidence would have to be very strong before he decides not to certify."

Hinton's remarks came as the Salvadoran government finds itself in an especially delicate and dangerous situation both politically and militarily.

An Army mutiny has left the military high command, long cultivated by Washington, in disarray, with a major reshuffling of senior officers expected shortly.

The guerrillas have launched a serious offensive from their northern and particularly their eastern strongholds and thousands of government troops are reportedly being moved into combat.

The guerrillas' Radio Venceremos said rebel forces had killed 35 soldiers and taken eight prisoners Monday in an advance to Meanguera, 12 miles north of San Francisco Gotera, the capital of Morazan province, United Press International reported.

Meanwhile, San Salvador is being crisscrossed by representatives from what one embassy staffer called a "flying circus" of 16 U.S. delegations here to make their own judgments about this government's human rights record, the war effort and Washington's support for it.

Senators and congressmen, doctors, lawyers and academics passed through last week. Members of the Moral Majority left yesterday; folk singer Mary Travers and actor Mike Farrell are due today.

State Department officials in Washington repeatedly have tried to convey the idea that certification is not a foregone conclusion. There were even attempts to soft-pedal President Reagan's remark in December after meeting with Salvadoran President Alvaro Magana that "of course" the certification would be granted at that time, given what Reagan knew then.

But Hinton, a senior Foreign Service officer with an exceptional degree of autonomy in this post, made it clear he dislikes the certification process and believes there is little choice as the law stands but to give this government the administration's seal of approval if that is the only way to keep vital aid flowing.

Hinton said the embassy's reporting is "objective" and that the current certification will be fair.

Several military leaders here have told the visiting delegations that they believe the certification process has been helpful in reducing human rights abuses and encouraging the development of a more democratic political system.

Hinton was critical of Congress not only for the certification law but for recent cutbacks in what he sees as already inadequate aid.

Congressional failure to pass $35 million in supplemental military assistance and a cut of $53 million for El Salvador from the Caribbean Basin Initiative will "give the guerrillas more hope" and "take the pressure off them," Hinton said.

Some of the congressmen who were responsible for the certification law were among the many official visitors to El Salvador in the past few days. They expressed interest in writing a new, tougher law that might include a requirement compelling the Salvadoran government to enter negotiations of some sort with the left.

Hinton declined to address the question of negotiations at any length, but Salvadoran officials make it clear that for the moment they remain unwilling to talk with the guerrillas for any purpose other than bringing them into the electoral process.

Sen. Christopher J. Dodd (D-Conn.) gave the basic rationale for the certification process when he told Salvadoran and foreign reporters that nobody in Congress wants to see a Marxist takeover here but that human rights problems have been so dreadful "nobody wants to be a party to that."

After the United States has spent millions of dollars, Dodd said Saturday, "there is a growing sentiment in the United States that we are not any better off here."

Looking at what he calls the "carnage" wrought in this civil war during the past 2 1/2 years, Dodd called for more international cooperation in getting talks started.

Dodd and other critics of administration policy here have acknowledged following the two previous certifications, in January and July last year, that the law as it stands leaves Congress little room to dispute the presidential assertion of progress here outside of an unlikely majority vote for a complete cutoff of aid.

Although Dodd said here that he had "serious questions" about whether the Salvadoran government had met the criteria for certification, he said he would withhold judgment until seeing Reagan's report.

On the crucial certification question of whether this government is "making a concerted and significant effort to comply with internationally recognized human rights" the debate in many cases has been reduced to disputes over body counts.

In all the counts conducted by human rights groups and by the U.S. Embassy there is a decline in deaths attributed to political violence from 1981 to 1982, but whether that is the result of less killing or less reporting is still disputed.

In this country of fewer than 5 million the lowest figure for deaths attributable to political violence is compiled by the embassy from press reports. It calculates 2,722 in 1982 as opposed to 5,331 in 1981. The highest estimate for 1982 is 5,399 civilian deaths ascribed to government forces by the legal aid office of San Salvador's archdiocese, down from about 13,300 in 1981.

On the politically sensitive investigation into the murders of four American churchwomen in December 1980 and of two American agrarian reform advisers in January 1981 there have recently been some noted setbacks.

The final trial of five members of the National Guard accused of killing the churchwomen is stalled by legal procedures, and lawyers for the victims' families do not expect it to begin until this summer.

One key suspect in the case of the agrarian reform advisers, an Army lieutenant with close ties to Assembly President Roberto D'Aubuisson, is back on active duty after a Salvadoran judge released him for lack of evidence.