SAN SALVADOR, OCT. 6 -- After two days of intense negotiations, a leftist rebel alliance and the government of President Jose Napoleon Duarte announced an agreement early today to establish two formal negotiating bodies charged with resolving El Salvador's eight-year civil war.

The four-member joint commissions are to be named within five days to produce agreements on a cease-fire and other points by Nov. 4, in accord with a Central American peace plan signed in Guatemala two months ago.

One commission is to concentrate on the thorny issue of arranging a cease-fire between the 56,000-member Salvadoran Armed Forces and the estimated 6,000 Marxist-led rebels of the Farabundo Marti National Liberation Front. The second commission is charged with reaching agreements on the other provisions of the regional peace plan, notably an amnesty, democratic reforms, a cutoff of foreign aid to insurgents and a ban on use of one state's territory to attack another.

While the agreement marked a significant step toward opening a regular peace negotiating process, and toward lessening mistrust, participants said, it left fundamental issues unresolved and produced no guarantees of an end to a civil war estimated to have cost more than 60,000 lives.

"Our positions and those of the government are very far apart," said Schafik Handal, one of the guerrilla commanders representing the FMLN in the talks.

Potential complications emerged soon after the accord was announced as both sides raised controversial elements in statements to reporters. Duarte said he planned to declare a unilateral cease-fire if the commission fails, and rebel leaders linked a truce to their longstanding demand to be included in a coalition government.

The announcement of the limited agreement came after the two sides concluded some 20 hours of talks in the residence of the papal nuncio. The meeting marked the first peace negotiations in three years and the first in the capital.

About 600 rebel supporters stayed past midnight in a vacant lot near the papal nunciature in an exclusive residential neighborhood. They were treated to the rare spectacle of a joint appearance by the eight-member rebel delegation, including four guerrilla commanders wearing military fatigues.

The rebels mounted a government-built stage and their two most senior members, Handal and political leader Guillermo Ungo of the Democratic Revolutionary Front, addressed the chanting crowd as government riot troops in helmets and flak jackets stood guard in adjacent streets.

In a news conference at the same time in a hotel a few blocks away, Duarte warned that if the cease-fire commission failed to agree on a truce by a Nov. 4 deadline, he would declare a unilateral cease-fire in order to comply with the Central American peace plan -- which calls for cease-fires in the region's wars and other pacification measures by Nov. 7.

"I am ready to assume the historic challenge of this document and ask the armed forces for a unilateral cease-fire," Duarte said. He said that as president and commander-in-chief of the military, he would guarantee the Army's compliance.

"I don't want to fool myself and be falsely optimistic, but I am hopeful that an agreement can be reached," Duarte said. He said he hoped the rebels would eventually realize that "the situation of the country has changed" and that now "there is a process of democracy.

"The path they {the rebels} have chosen once had justification, but today it doesn't have justificaion."

In his remarks last night to the pro-rebel crowd of peasants, students and workers, organized by a leftist union, Ungo declared, "Our presence signifies the recognition that we are a belligerant force without which it is not possible to decide the destiny of our country."

In a halting speech marked by awkward silences, Handal, the leader of the Salvadoran Communist Party and the eldest of the four guerrilla commanders present, said, "Our position on a cease-fire is very distant from the position of the government. For us a cease-fire is linked to a solution that resolves the principal and fundamental aspects of this conflict." He added that "we do not want to raise false expectations."

As the rebel leaders spoke, the crowd waved red flags and shouted slogans in support of the FMLN and against Duarte, the Salvadoran military and the United States.

In a news conference this morning at the Spanish ambassador's residence, the rebel leaders stuck by longstanding positions and made it clear that a cease-fire would be difficult to achieve. Specifically, they said had not dropped their demand for participation in a "transition government" pending new general elections -- a demand that Duarte has rejected.

"We don't think a cease-fire can be isolated from the entire problem," Handal said. "A cease-fire implies the recomposition of the government, incorporating all national sectors without distinction."

Handal also said that any eventual cease-fire should include "guarantees" so that neither side could use it to strengthen itself militarily. He said this meant a "moratorium" on arms deliveries, the halting of recruitment by both sides and the withdrawal of foreign military advisers. Currently, more than 50 U.S. military advisers are assigned to El Salvador.

Handal and leaders of the Democratic Revolutionary Front insisted that a "transition government" could be formed without scrapping El Salvador's existing constitution, which Duarte has repeatedly vowed to uphold, and without unseating him as president.

Handal added later, however, that "as long as the war goes on, our aim will be to depose Duarte and his government." He and the other rebel leaders dodged questions about what they would do in the event Duarte declared a unilateral cease-fire.

After the two-hour news conference on the portico and lawn of the spacious ambassadorial compound, Gonzalez and another rebel commander were to be driven back to their mountain strongholds in a caravan escorted by Red Cross officials and diplomats. The other rebel representatives were expected to leave by plane for Panama.