Will El Salvador's authorities be moved to reform by a top defense official from the superpower whose military aid is supposed to be conditional on that reform? The Reagan administration deserves credit for at least giving it a try by sending down Fred Ikle with a latter-day message to Garcia. In this case it's Defense Minister Garcia, and Under Secretary of Defense Ikle was reportedly charged with letting him know that the aid will end under congressional pressure unless the human rights situation gets better.
Any number of Salvadoran excesses could earlier have brought such high-level attention from Washington. For example, Amnesty International's just released annual report for 1982 identifies regular security and military units as responsible for ''widespread torture, mutilation and killings of noncombatant civilians from all sectors of Salvadoran society.''
The present timing of the Ikle mission follows two recent publicized episodes - and precedes the January deadline when President Reagan must certify to Congress once more that El Salvador has made sufficient progress on rights to warrant continued US aid. The visit also occurs just when the US had seemed to be more open to negotiations between the right-wing authorities and the left-wing opposition backed by guerrilla forces. And just after Salvadoran leader Roberto d'Aubuisson rejected a rebel offer of ''direct dialogue'' without preconditions, which followed the freeing of 44 captured government soldiers.
The possibility of negotiation must be kept alive even as attention focuses on the two episodes that triggered Mr. Ikle's trip:
* One was the apparent abduction of 15 opposition and labor leaders by heavily armed men in civilian clothes. The military finally acknowledged that eight of the victims had been arrested and would be tried for terrorism. The fate of the others was not disclosed. It might be noted that the Inter-American Commission on Human Rights has made the basic point that state terrorism is not an acceptable means of combatting subversive terrorism.
* The other immediate episode involved judicial failure to try certain suspects in the murder last year of two US land-reform consultants and a Salvadoran land official.
After the US message to Garcia, Congress will be much interested in Mr. Ikle's message from Garcia. It will take evidence of genuine human rights progress to keep the next controversy over certification from being even sharper than the last.