The Reagan administration reported to Congress yesterday that, despite major difficulties, the government of El Salvador is making enough progress toward economic and political reforms to justify a continuation of U.S. military assistance.

This certification, in the form of a 48-page report from Secretary of State George P. Shultz, is required by law every six months to keep military aid and arms sales flowing to that country.

The report acknowledged that "severe civil strife" and violence from all sides continues in the Central American country, where early last year the Reagan administration, and especially then-secretary of state Alexander M. Haig Jr., vowed to draw the line against communism in this hemisphere.

"We continue to be concerned over the human rights situation and the course of the reform program in El Salvador. Nevertheless, there are tangible signs of progress . . . and we believe a firm base has been established for further progress in the months ahead," the document said.

The report described the March 28 elections as "the most important development in El Salvador in recent months" and said "the development of democratic order" is in the long run likely to be the best guarantee of human rights.

Reflecting opposition to the existing land reform program among some of those elected, especially the forces led by Constituent Assembly Chairman Roberto D'Aubuisson, the report said land reform was "relaunched" by others in the government and the military.

Critics inside and outside Congress immmediately attacked the certification. Sen. Christopher J. Dodd (D-Conn.) called the report a "sham" and said it will provide a green light for Salvadoran government leaders "to do anything they damn well please."

Reps. Tom Harkin (D-Iowa) and Gerry E. Studds (D-Mass.) announced that they will introduce legislation today to reject the certification, on grounds that it is neither accurate nor in good faith.

Rep. Stephen J. Solarz (D-N.Y.), a sponsor of the certification requirement, called the report "unwise and unjustified." The United States should be working for a negotiated settlement rather than continuing to support a brutal regime, he said.

The American Civil Liberties Union and Americas Watch Committee issued a statement of "deep regret" at theaction, charging that it "ignored the requirements of the law and distorted the reality" in El Salvador. The two organizations issued a 272-page report last week charging the Salvadoran government with a campaign of "systematic political murder" that disqualifies it from receiving further U.S. aid.

Two aspects of the report caught some critics by surprise. It was issued one day earlier than expected, July 28 being the deadline for the semi-annual certification, and it was signed by Shultz even though the foreign aid law requires the report to come from the president.

State Department officials said Reagan had delegated the chore to Shultz, a commonplace practice in required reports to Congress. Last year senior White House aides took steps on several occasions to shield Reagan from being involved directly in this most controversial of his foreign policies. White House and State Department aides denied, however, that the absence of Reagan's name was intended to disassociate him from the Salvadoran policy.

Under the law passed late last year, the president was required to certify every six months that progress is being made by the Salvadoran government on four issues: human rights, control of the armed forces, land reform, and political solutions, including elections.

An additional requirement, which was passed by the Senate at about the time the report was going to Capitol Hill yesterday afternoon, calls for the administration to show that Salvadoran authorities had made progress in bringing to justice the slayers of four U.S. churchwomen and two labor advisers.

In a briefing for reporters, a senior State Department official declared, "We call it as we see it," and said the report reflects substantial efforts by the Salvadoran government in all the areas covered.

Under questioning, the official refused to discuss a story that gruesome torture was recently inflicted on a Salvadoran Green Cross volunteer in a secret suite of torture rooms at National Police headquarters in downtown San Salvador. The official, who cannot be quoted by name under the rules of the briefing, said U.S. authorities had taken "several allegations" of torture to Salvadoran officials during the past six months.

Assistant Secretary of State Thomas O. Enders will be the senior State Department official defending the report in hearings to begin Thursday in the House Foreign Affairs Committee. Hearings in the Senate are to begin next Tuesday.

Among the report's points: Human Rights

"Severe civil strife has continued in El Salvador in the period covered by this report. The newly elected Government of National Unity continues to be engaged in a struggle with a guerrilla movement which, with external support, is attempting to seize power by force. This strife in El Salvador continues to produce serious and frequent violations of basic human rights committed by leftist guerrillas, right wing terrorists, and members of the government's military and security forces.

"Indices of political violence, from whatever source, are uncertain....According to the various available sources, however, there has continued to be a downward trend in the monthly totals attributable to political violence during the past six months...

"Although abuses continue, there has been a demonstrable attempt on the part of government authorities to control forces which perpetrate them....The embassy has been able to confirm that since Jan. 1, 47 members of the military forces and at least 10 civil defense members have been arrested and confined for violent abuses of authority (murder, assault, rape). Of these, 20 were arrested for murder." Armed Forces

"There continue to be reports of human rights abuses on the part of various branches of the Salvadoran security forces. Although there has been no evidence to support periodic guerrilla allegations of large-scale massacres allegedly committed by government forces, reports of torture and execution of prisoners and the participation of individual members of the security forces in right-wing terrorist activity continue, and in some cases are credible...

"In an effort to cope with the problem of official abuses, the Minister of Defense, Gen. Jose Guillermo Garcia, issued instructions in March to all military personnel stating that violators of the military code of conduct will be disciplined....The National Police have recently redrafted an exhaustive guide on counterinsurgency procedures....The International Committee of the Red Cross gives instruction to the security forces on respect for human rights in armed conflict as defined in the Geneva Convention." Land Reform

"While the major land distribution accomplished under Phase I proceeded smoothly during this certification period, the Phase III land reform program has been through a tumultuous process....During the post-election period, elements opposed to the reforms in the Constituent Assembly took advantage of an effort to correct some of the program's shortcomings to pass ambiguous legislation which...contributed to a surge of illegal evictions.

"The government, with full cooperation of the military, immediately took steps to correct the situation. The ambiguous legislation was clarified. The application process was resumed, promotion campaigns began again, the first definitive titles were issued...the Salvadoran armed froces have returned more than 1,900 farmers and their families to their land since June 1."