The Rev. Roy Bourgeois, an American Maryknoll priest missing and presumed dead here for the last 12 days, today walked in from the countryside, where he said he was talking to peasants, and turned himself over to the U.S. Embassy.

Bourgeois's sudden reappearance coincided with the release only hours earlier of a delayed letter from him explaining that he had decided to "join with the poor of El Salvador in their struggle for justice and peace."

The return of Bourgeois, a 38-year-old priest from Chicago, was announced officially tonight by U.S. Embassy spokesman Howard Lane.

Speaking to reporters before the sandbagged gates of the embassy here in a news conference that was interrupted by a bomb explosion only several blocks away, Lane said Bourgeois "is very much alive and well and of course we are very happy to see him in that condition."

Lane said the priest, who had disappeared from his hotel here Sunday morning, April 26, was being provided with a place to stay tonight and would be returning to the United States "as soon as possible," presumably Thursday.

The spokesman said Bourgeois, who had a fresh haircut but appeared tired and unshaven, would make no statements before his departure. Nevertheless, Lane revealed that Bourgeois told U.S. officials that "he had been in the campo, the countryside, talking to campesinos [peasants] and he would discuss his experiences when he gets back to the United States."

Officials did not explain why Bourgeois went 12 days without communicating that he was alive amid widespread fears that -- like other priests and nuns who have disappered here before -- he had been killed. Those fears prompted the intervention with President Jose Napoleon Duarte of Secretary of State Alexander M. Haig Jr. and the head of the Maryknoll order, the Rev. James Noonan, who flew here last week to investigate. [United Press International quoted Ronald Saucci, a priest in the Maryknoll mission in Ossining, N.Y., as saying Noonan spoke with Bourgeois about 8 p.m. EDT. "We've been praying very hard" for Bourgeois' safety, Saucci said. "Thank God our prayers were answered."]

According to the embassy spokesman, Bourgeois said the letter announcing his support of the poor and dispossessed here and attacking U.S. support for the civilian-military junta that Duarte heads went astray. "He said he had intended that the letter be delivered several days earlier to explain his mysterious disappearance," the spokesman said. "It was an authentic letter, but it was not delivered until today for reasons that were beyond his control."

The letter was delivered in a secret rendezvous behind a church here early this afternoon to a Salvadoran journalist. The journalist said the man who gave it to him resembled Bourgeois, although spokesman Lane said tonight that it was not.

The letter said, "After much reflection and prayer, I have decided to join with the poor of El Salvador in their struggle for justice and peace."

The letter indicated that although Bourgeois was siding with the guerrillas, he would not personally take up arms. "Though I recognize that the armed struggle of the Salvadoran people is justified," the letter said, "I personally cannot and will not take up arms." Bourgeois, a Vietnam veteran born in Lutcher, La., returned from the war to be ordained as a Maryknoll priest and has been a advocate of nonviolence and the defense of human rights.

Although he previously had worked as a priest with the poor in other Latin American countries, Bourgeois came only temporarily, on his own, to El Salvador, where a number of Maryknoll priests and nuns have been assigned by their order.

Members of the order have been attacked verbally and threatened by conservative forces here, and two Maryknoll nuns, along with an Ursuline sister and an American lay worker, were murdered here last December. Although the case remains officially unsolved, U.S. diplomats have indicated that evidence gathered thus far has implicated members of the Salvadoran security forces.

In the controversy surrounding those murders and U.S. backing for the Salvadoran military-civilian government, high-level officials in the Reagan administration have suggested that there may be some justification in right-wing Salvadoran charges that U.S. Roman Catholic clergy may be actively supporting the left there.

The Maryknolls, backed by the U.S. Catholic Church in general along with a wide spectrum of congressional leaders and human rights activists, have heatedly denied the charges while sharply criticizing U.S. military aid to the Salvadoran government.

Stating that it "hurts me deeply" to know that his country, the United States was sending military advisers and weapons to the Salvadoran government, which he labeled a "repressive dictatorship," the letter called on the American people to oppose any U.S. intervention in El Salvador.

"I ask the people of the United States to join with our brothers and sisters of El Salvador," Bourgeois wrote, "to do everything it can to prevent the military intervention of the United States in this country. We need rice and beans -- not weapons."

Bourgeois said that the issue in El Salvador is not communism, adding: "It is more a case where the poor and the oppressed are fighting for food, for existence."

The priest had flown to El Salvador April 23 with a team from WBBM-TV, a Chicago CBS affiliate. After three days in which he acted as an interpreter for the television station, he went to Sunday mass at San Salvador's cathedral, then told colleagues at the Hotel Camino Real, where he was staying, that he was going across the street to a pharmacy to buy medicine for an upset stomach. He had not been heard from since.

An unidentified caller telephoned a Salvadoran journalist today, and set up the rendezvous behind the church. The caller told the reporter, who did not want his name used, to pick up a package. When the journalist got there, he saw five men in a small German sedan. A man whom he later identified from photographs as Bourgeois, wearing a brown shirt and had a cap pulled down over his usually sandy and curly hair, extended an envelope to him and said "this is to be publicized."

The men then jumped in the car and sped away.

The letter was shown to U.S. diplomats at the American Embassy who said it was the first they had heard about it. Later comparisons made by journalists of the handwriting and signature with restaurant receipts seemed to confirm that it was written by Bourgeois.