Guatemala's new ruling general lifted formal restrictions on civil liberties today in his first initiative since overthrowing President Efrain Rios Montt in a military coup.

Gen. Oscar Humberto Mejia Victores, defense minister and now chief of state, issued the decree abolishing Rios Montt's "state of alarm," ending censorship and abolishing controversial secret tribunals as Army troops in battle gear deployed in several places to guard against any uprising by opponents of yesterday's takeover.

The decree marked the first concrete demonstration of Mejia's promises to carry out the political liberalization that Rios Montt had pledged when he came to power in a similar military coup March 23, 1982, but never fully carried out during his 16 months in office.

Guatemalan political sources and other observers said the extent to which Mejia maintains the impression that he really intends to carry out such a political opening will go a long way toward determining whether his takeover will lead to elected civilian rule and stable government or prompt yet another chapter in Guatemala's history of military takeovers.

U.S. Ambassador Frederic Chapin held a brief meeting with Mejia at the ruling general's home here, underscoring Washington's apparent willingness to work with the new leader despite earlier support of Rios Montt and a declared policy of opposition to violent changes of government.

In Washington, State Department spokesman John Hughes said Mejia had told Chapin of his plans to restore civil liberties during their meeting. Hughes called the changes "positive steps which the United States fully supports."

Chapin said after the meeting with Mejia: "We discussed his program of government set forth in his remarks yesterday and his desire for close dialogue with representatives of the United States government. That began today."

Mejia assured Chapin that no reprisals will be taken against Rios Montt who remained secluded under what amounted to house arrest at an unknown location in Guatemala City. Mejia said yesterday that Rios Montt, 57, has been placed in "military availability," meaning he is retired from official duties but continues to draw a salary.

Mejia, 52, also provided Chapin with indications that he intends to accelerate the electoral timetable that had been under consideration by Rios Montt and denounced as too slow by Guatemalan political leaders and the country's officer corps. Rios Montt had promised elections for a constitutent assembly next July. Without making firm commitments, he had held out the hope of presidential elections by late 1985 and inauguration of an elected leader in 1986.

Mejia had visited the U.S. aircraft carrier Ranger Sunday, conferring with U.S. military officials and fellow Central American defense ministers. Rios Montt was to visit the Ranger yesterday and two U.S. Navy planes were awaiting him at the Guatemala City military airport when Mejia's forces carried out the coup. The Ranger was sent to Central America as part of the Reagan administration's show of force to deter what it describes as Soviet and Cuban intereference in Central America.

Chapin drove to the airport while the military showdown was in progress in case Rios Montt showed up, knowledgeable sources said. When he failed to arrive as scheduled, the sources said, Chapin returned to the embassy and followed developments in the coup.

Maj. William Mercado, the embassy's assistant military attache, was seen at the presidential palace during exchanges of fire yesterday between Mejia's forces and loyal presidential guards. Mercado carried a walkie-talkie to keep the embassy informed blow by blow as the coup was carried out, the informants said.

Vinicio Cerezo, leader of Guatemala's Christian Democratic Party underscored the importance of Mejia's pledge to return to democratic government.

"I think if there are not elections in one year, there is going to be instability again," he said in an interview.

Cerezo said in an interview that some political leaders are urging Mejia to drop the idea of a constituent assembly vote and proceed directly to presidential elections next July.

Cerezo said that Guatemalan political circles had expected a military coup for weeks and it was widely known that Mejia had been selected by the officer corps to become chief of state once Rios Montt was removed from the presidential palace. The Christian Democratic Party, he said, more than two weeks ago drew up the statement issued this morning laying out its position on Mejia and his coup. The U.S. Embassy, which exercises considerable influence here, had in recent weeks reduced its previous opposition to a military coup, thus encouraging the officer fraternity to act, Cerezo said.

"They did not support the coup, but they appeared neutral," he added.

Official Guatemalan reports said two persons were killed during the clash, one child hit by a stray bullet and one Army officer. Other sources with close contacts in the Guatemalan Army said up to five persons were killed, including several soldiers, and a dozen were injured. Official reports yesterday had said only one person was killed and one injured.

Rios Montt first told Mejia he would step aside without resistance when the defense minister challenged him at about 9:30 a.m yesterday, reliable informants said. But then, inexplicably, the often eccentric leader changed his mind and ordered his guards to resist. At one point, a helicopter exchanged fire with ground units, sources said, during a fight that lasted about half an hour until Rios Montt agreed to leave peacefully.

Mejia acted in concert with the main Army leadership, according to Guatemalan and foreign sources.

One factor in the decision to act yesterday was that at least two other coup plots were under discussion, risking division and perhaps conflict in the armed forces, they said.

Representatives of the country's main right-wing political group, the National Liberation Movement led by Mario Sandoval Alarcon, were in contact with allies in the officer corps who were trying to organize a coup, the sources said. They added that some of the young officers who helped bring Rios Montt to power also were discussing a possible move to bring him down.

Among the main complaints from all sides was Rios Montt's refusal to carry out demands presented to him during a near-coup June 29. Chief among them, Guatemalan and foreign sources said, was the demand that he dismiss two chief aides who are, along with Rios Montt, elders of the fundamentalist Protestant Church of the Word.

The two, Francisco Bianchi and Alvaro Contreras, were quickly dismissed by Mejia, a Roman Catholic. The new president also held a joint news conference with the acting archbishop of Guatemala, Ramiro Pellecer, who called for an end to religious division in the country. Two of Rios Montt's military advisers, Cols. Mario Rene Enriquez and Victor Manuel Argueta, who had drawn resentment among their fellow officers by handing out orders from their offices in the presidential palace outside the chain of command, were sent back to their units yesterday.