A high Pentagon official arrived here today for talks with the Salvadoran leadership in an atmosphere of concern over the secretive arrests of key leftist politicians and union leaders during the past two weeks.

Fred C. Ikle, undersecretary of defense for political affairs, scheduled meetings with Defense Minister Jose Guillermo Garcia and President Alvaro Magana, among others, as part of a brief visit billed as an inspection of U.S. military assistance to the Salvadoran Army in its battle against rebels backed by neighboring Nicaragua.

Ikle also was expected to express official U.S. concern over the roundup of opposition figures. More than a dozen persons, including five prominent leftist politicians and several union activists, have been abducted since rebels of the Farabundo Marti National Liberation Front two weeks ago launched their broadest series of attacks since the Salvadoran elections last March.

In Washington, State Department spokesman John Hughes said Ikle's visit "is a familiarization trip that had been postponed several times. It is on the U.S. assistance program . . . I'm sure that in the course of his discussions he will bring up the human rights question."

The Reagan administration, which has made El Salvador the focus of its Central American policies, is eager to avoid such situations that leave the Salvadoran government open to charges of human rights violations. To continue its aid, the administration must certify to Congress every six months that El Salvador is making progress on human rights.

The next certification is due in January. Tensions over the issue already have been heightened by pressure for resolution of the murder of two U.S. land reform consultants in San Salvador on Jan. 3, 1981. The investigation is being watched in Congress as a measure of the rights situation.

The recent arrests focus another spotlight on the issue. Carried out in secret, the arrests became known first through complaints from family and friends of those taken away. U.S. Ambassador Deane R. Hinton said Saturday he did not believe the government had done it and that, despite queries to government security forces, he had no idea why the arrests were made or by whom.

On Monday, U.S. diplomats here were expressing doubt that the government could have carried out the arrests. But later that day, the Defense Ministry said it had arrested eight persons on charges that they "participated in, organized and are leaders of illegal terrorists groups that have brought mourning and pain to the Salvadoran family and who are working through acts of vandalism for the destruction of the national economy."

The legal aid office of San Salvador's Roman Catholic archdiocese reported that in all, 11 persons have been rounded up since the guerrilla offensive began Oct. 10. Most were picked up by plain-clothed gunmen, it added, and the victims were active in groups with ties to the Democratic Revolutionary Front, the rebels' political arm.

Leftist sources identified the most prominent of those arrested as Mauricio Antonio Domenech, a leader of the National Revolutionary Movement; Carlos Molina, an economics professor and leader of the Independent Movement of Professionals and Technicians, and David Elias Guadron, of the National Revolutionary Movement.

A leftist-oriented cleric assessed the arrests as an attempt by rightist elements in the Army to prevent any chance of dialogue between the rebel movement and the government. The country's insurgent movement called yesterday from Mexico city for talks with the government about a five-point plan it said could bring an end to El Salvador's 3-year-old civil war.

"They are eliminating the possibility of a dialogue," he said. "I don't mean [President] Magana or [Defense Minister] Garcia, but certain parts of the right wing of the Army."

Magana has said he would accept dialogue with the rebels only if they first lay down their arms. His position coincides with that of the Reagan administration, which has said the rebels should get involved in elections scheduled for 1984 if they want to be part of the government. Rightist leader Roberto D'Aubuisson rejected the call yesterday.