Confusion erupted within the Salvadoran guerrilla political arm yesterday over the future of talks with President Reagan's special ambassador, Richard B. Stone.

After a flurry of international telephone calls, denials and retrenchments, the group finally admitted to "a problem of communication" last night and agreed on a relatively mild condemnation of Central American military exercises Reagan launched last month.

The incident demonstrated the five fractious rebel groups' continuing problems in reaching agreement on the issues that divide them from the rightist government of El Salvador that they are trying to overthrow.

Alberto Arene, U.S. spokesman for the political wing of the Farabundo Marti National Liberation Front/Democratic Revolutionary Front (FMLN/FDR), telephoned the media in late afternoon to say that future talks with Stone would be conditional on the withdrawal of U.S. forces from the military exercises.

He read a long formal statement from the group that would have been a major blow to the budding dialogue. But when Ruben Zamora, chief of the guerrillas' political arm, was reached by telephone in Managua, Nicaragua, he expressed mystification and then rejected the position.

"That does not represent the views of the alliance," he said.

Several hours and phone consultations later, Arene called reporters again to revise his statement. "There exists a total consensus" among the five groups "that the presence of these ships and troops does not create conditions that favor the said dialogue," he said.

The earlier ultimatum, he said, was the official position of only one of the groups, the National Resistance. He said "members of the alliance" had told him incorrectly that all the other groups had agreed to it. "There is still discussion," he added. "The distance makes it hard for us to coordinate. There was a problem of communication."

State Department officials remained ignorant of the entire episode, saying the guerrilla alliance had not contacted them.

Stone met with Zamora July 31 in Colombia. Both sides expressed hopes then that this was a prelude to talks involving the Salvadoran government and the full guerrilla leadership.

The confusion apparently arose from the rebels' desire to counter Reagan's assertion that his tough stance in Central America has led to a softening of the leftists' position and new flexibility on related matters in Nicaragua and Cuba. "Reagan tells everyone his policies are helping the dialogue, but it's really totally the contrary," Arene said.

Arene's initial statement charged Reagan with using the Stone mission "to buy time and political space to advance his military plan . . . , not to construct peace, but to cover, facilitate and make war."

"The FMLN/FDR conditions the dialogue . . . on a withdrawal of the ships and troops of war and intervention that threaten the regional peace," the statement said. "Dialogue ought to be an instrument of peace and not of war."

At the same time, other sources close to the negotiations said a date and time for the next meeting with Stone already had been set. The sources said the talks would be soon but they would not give a date.

In a related matter, Salvadoran Peace Commission president Francisco Quinones said Thursday that the first meeting between the guerrillas and the government will occur "before the end of the month."

In an interview with the Los Angeles Times, Quinones declined to give the place or date of the meeting, but said two sets of letters had been exchanged with the guerrillas since May, and that they had agreed in writing July 12 to talk.

"I hope a dialogue will be established in subsequent sessions," Quinones said.