A closed conference here of military commanders and intelligence officials from 20 countries in Latin America and the Caribbean has heightened already strong suspicions in Cuba and Nicaragua that the United States is planning or promoting military operations against their countries.

U.S. officials have been stressing that the Conference of American Armies, which gathered to discuss "countering terrorism, subversion and armed insurrection," was not called by the United States or intended for the planning of new U.S. military initiatives, but is the 14th in a regular series of meetings of U.S. and Latin military leaders.

Nevertheless, Nicaragua released a letter protesting its exclusion from the meeting, and a Nicaraguan official here charged yesterday that Managua was scheduled to attend until it was moved from Panama to Washington last summer.

Meanwhile, Cuban United Nations Ambassador Raul Roa Kouri delivered a note to U.N. Secretary General Kurt Waldheim protesting what he said were U.S. plans to blockade or bomb Cuba.

The conference, which opened at Ft. McNair on Tuesday and closed yesterday afternoon, was held in strict privacy -- Pentagon officials declined to discuss even the two keynote addresses delivered by Defense Secretary Caspar W. Weinberger and Salvadoran Defense Minister Jose Guillermo Garcia -- and a statement cited "the classified nature of the issues to be addressed."

However, U.S. officials familiar with the text of Weinberger's speech said the United Stress was stressing the need for solidarity among the attending governments against the perceived threat of Cuban and Nicaraguan influence and insurgency in Central America and the Caribbean.

A number of Latin American diplomats here said the conference focused specifically on El Salvador and U.S. charges of Nicaraguan and Cuban involvement there. The administration indicates an ongoing war there between U.S.-backed government forces and leftist guerrillas has reached a stalemate, and other reports from El Salvador itself indicate increasing guerrilla advances.

Some administration officials say the government of Salvadoran President Jose Napoleon Duarte appears close to collapse. Last week, Secretary of State Alexander M. Haig Jr. said that "extensive studies" recently had been completed within the administration on ways to deal with the situation and thwart what is perceived as increasing Cuban subversion in the hemisphere.

Washington's increasing sense of urgency over the Salvadoran crisis, and the secretive atmosphere surrounding this week's military conference here, have helped to persuade Cuba and, to a lesser extent, Nicaragua that the United States is planning to intervene in the region, according to diplomatic sources.

The anticipated intervention, diplomats in both countries and published accounts in Cuba's government-run press said, could come from any of several directions, including direct military involvement in El Salvador, a punitive strike against Cuba or Nicaragua by U.S., Latin or exile forces, or a naval blockade of either or both countries.

The United States has not responded to any of the speculation as to its specific intentions, or, according to Nicaraguan and Cuban diplomats, to direct queries from those governments. Argentina, the country whose military government is most often mentioned as a possible back-up or surrogate force for the United States in Central America, has in the past denied it would introduce any troops or trainers into El Salvador.

Thus far, the only hint of a move in the direction of new military assistance to the Salvadoran armed forces has come from recent meetings between high-level officials of the Salvadoran government and the military governments of Guatemala and Honduras. Both those governments have denied that they intend to become involved in El Salvador.

Roa told reporters in New York yesterday, "I believe that there is a danger of either a naval blockade, of economic actions, or of persecuting the companies that do business with us, and even of an air strike against key economic points of Cuba." The State Department refused to comment on his statement.

A switch of the conference location from Panama City to Washington last summer, reportedly made because Panama did not want to bear the cost of the meeting, apparently was followed by the exclusion of Nicaragua, which under the dictatorship of Gen. Anastasio Somoza hosted the American Armies conference in 1977. Col. Donald Mendoza, the military attache at the Nicaraguan Embassy here, said yesterday that Nicaragua had been refused when it requested a U.S. invitation.

A letter dated Aug. 22 from U.S. Gen. Peter M. Dawkins, the secretary general of the conference, to Mendoza explained that Nicaragua could not attend because "the attendees must share common perspectives on security and defense issues of mutual interest within the boundaries of the American hemisphere."

U.S. officials also pointed out yesterday that Nicaragua did not attend the last American armies conference, held in 1979 in Bogota, Colombia.