El Salvador's newly formed civilian-military Junta today called on leftist groups to "incorporate themselves, in our government . . . and have confidence in our intentions," but warned that "public order" would be protected against political violence.

In a two-hour news conference, the-five man junta also said presidential elections would be held before the previously scheduled 1982 date, and that "we don't intend to stay [in power] very long."

The junta said El Salvador would establish relations with Cuba, and denied speculation that the United States or any other country helped put it in power.

Other than a brief statement last night announcing three civilian members of the junta, today's news conference was the first public appearance of the full government: a mixture including two young Army officers, a U.S.-educated engineer, a center-left politician and a local businessman.

Central America's newest committee government joins ruling juntas in Nicaragua and Honduras, and has also promised sweeping social and economic forms. But its members admitted that t heir intentions outnumbered substantive plans at this point.

Yesterday, the junta issued a decree ordering all political prisoners freed in eight days. Today, both Roman Mayorga, an engineer and university rector, and Col. Jaime Abdul Gutierrez, one of two military officers in the junta, said they had never been inside any of El Salvador's prisons, and did not know how many, if any, political prisoners there were.

According to the office of San Salvador's archbisop, 198 suspected government opponents disappeared over the past three years, 94 of them in 1979. The previous administration, headed by ousted Gen. Carlos Humberto Romero, denied secretly holding political prisoners.

The junta said it would name a commission, including Archbishop Oscar A. Romero -- no relation to the ousted general -- and the local " committee of Mothers" of persons who have disappeared. The commission would inspect all jails and look for those who have disappeared.

Another commission would be formed, Col. Adolfo Arnoldo Majano said, to investigate military and police officials of torture and murder under the Romero government.

"What we have agreed on," Mayorga said of the junta, "is that only real change would come by changing existing social and economic structures, and with effective popular participation" in the government.

Under Romero and other military presidents since 1933, El Salvador had developed an economy in which both money and land remained primarily in the hands of a small civilian oligarchy, protected by a largely corrupt military establishment. Repression of political opponents and traditional electoral fraud had given rise to growing violence and the development of illegal leftist organizations.

Asked how the junta will respond if violence continues, Guillermo Ungo, head of the social democratic National Revolutionary Movement, said the junta has established "a new, different government that is going to make a break with the past, that considers human life the most essential thing for human coexistence."

But both the civilian and military members of the junta appeared to agree that the government had an equal duty to preserve public order.

"We have called on the extremist groups to incorporate themselves," Gutierrez said, "and we want everyone to participate." Organizations -- including three large federations of peasants, student and union groups the previous government had branded subversive -- will be recognized, the junta said.

"But at the same time," Gutierrez said, "we have a duty to protect the citizens. What we guarantee is to respect" human rights.

Most of El Salvador was calm today. Organizations opposed to the coup on grounds it is a continuation of military power clashed earlier in theweek with security forces in confrontations that resulted in at least 16 deaths.