Secretary of State George P. Shultz is not known for agonizing over difficult decisions. Mr. Shultz's reputation is for being unflappable. But State Department officials say that when Shultz made the final decision to certify that El Salvador met the legal requirements for continued American aid, he agonized indeed.
''It was a closer call than most people realize,'' said a State Department official, noting that Shultz did not make his decision until close to the certification deadline, late Wednesday. It wasn't just a pro forma decision, the official said.
The law requires that President Reagan certify that the government of El Salvador is, among other things, ''making a concerted and significant effort to comply with internationally recognized human rights'' and that it is acting to bring to an end the torture and murder of Salvadorean civilians. The President's authority to make the certification was delegated to the secretary of state.
Without that certification, aid would be cut to a government that is fighting a war against leftist-led guerrillas and is heavily dependent on American assistance.
The problem for Shultz is not only that human rights progress in El Salvador, such as it is, has been painfully slow, but also that by the State Department's own account, the number of civilian deaths attributed to ''political violence'' has risen since the last certification of six months ago. The number of deaths per month is down from '81 and early '82.
''Armed rightist terrorists, including some members of the government's security forces, bear responsibility for many deaths attributable to political violence,'' says a State Department report submitted by Shultz to the Congress.
Some congressmen have suggested that a serious threat by the administration to cut off all aid to El Salvador might induce the Salvadorean military and security authorities to make a greater effort to bring human rights abuses under control. But congressional specialists say that such a threat would not be credible, because the Reagan administration is currently trying to increase aid to El Salvador.
A State Department official suggested that the only solution to the problem of human rights violations in El Salvador would be for the country to elect to office a civilian president who would hold greater powers than those now held by President Alvaro Magana. But the official added that the situation was complicated by a nationalistic reaction from some prominent Salvadoreans, both civilian and military, who resent being told what to do by the US Congress.
In his letter to the Congress, Secretary Shultz said it was evident that the Salvadorean government's record ''falls short of the broad and sustained progress which both the Congress and the administration believe is necessary for the evolution of a just and democratic society in El Salvador.
''I am particularly concerned by the failure of the government of El Salvador to achieve more positive results in establishing discipline over the security forces and in assuring that those, military or civilian, who commit gross violations of human rights will be brought to justice and held accountable under the law.''
In reference to seven US citizens who have been murdered in El Salvador, Shultz said that an ''especially compelling aspect'' of his concern was the ''slow progress made thus far by the Salvadorean authorities'' in bringing the murderers of these Americans to justice.
But the secretary concluded: ''The evolution of democracy is a long and difficult process, especially when there are concerted efforts to defeat it. As we have seen, in El Salvador progress in some key areas has been disturbingly slow. However, our disappointment over the pace of change should not obscure the fact that change is occurring. The people of El Salvador deserve our support in their effort to achieve a truly democratic society, which will provide the best and most lasting safeguard of human rights.''
As examples of progress, the State Department's 32-page report to the Congress says that the Salvadorean government has: released more than 500 prisoners; begun to reform its judicial system; and continued progress in implementing political and economic reforms, including land reform. It is also committed to holding elections late this year, and has formed a peace commission to bring all factions, including the guerrillas, into elections.
No one in either the executive or legislative branches of the US government seems to be satisfied with the certification process, whose main aim is to end human rights violations. Some congressmen are likely to try to tighten certification requirements.
Rep. Clarence D. Long (D) of Maryland, a key subcommittee chairman involved in battles over aid to El Salvador, said that it might be possible to rewrite the law to require more in the way of ''deeds'' rather than ''efforts'' from the Salvadorean government.
The congressman said that the most helpful event to occur recently was the Salvadorean government's release of some 540 prisoners. But he said that increases in assassinations over the recent six-month period was ''very disturbing.'' Mr. Long noted that not a single member of the military or security forces had ever been tried or convicted for such a crime.
''The human rights situation is dreadful,'' he said.
Long said his aim was to ''give enough military aid so they can force the guerrillas to negotiate, but not enough aid so that the government can go for a military solution.''