SAN SALVADOR, OCT. 5 -- Leftist rebels and the government of President Jose Napoleon Duarte met late into the night today for a second round of negotiations aimed at ending an eight-year civil war. A spokesman for the meeting said the two sides were embroiled in "in-depth" discussions of major problems.

After more than six hours of talks following a late start yesterday, the two sides decided to extend the meeting by a day. They convened again this morning at the Vatican mission here amid a news blackout.

Roman Catholic Auxiliary Bishop Gregorio Rosa Chavez, who is serving as spokesman for the church-sponsored talks, said the two sides had "not set a time limit" and were "working with an open agenda." After nine hours of talks, the delegations were still inside the building.

Asked if a cease-fire in the civil war had been discussed, Rosa Chavez said, "I can only tell you that we are discussing important problems in depth."

Diplomats said it was a good sign that the government delegation headed by Duarte and the representatives of a rebel alliance had agreed to continue talking today. They said the probable best result from the meeting, the first such talks since two negotiating sessions ended in failure in 1984, would be an agreement to meet again and turn these contacts into a long-term process for a negotiated solution.

"This is the most significant moment politically in El Salvador in the last three years," a European diplomat said. However, he added, "the positions on both sides have not changed one iota, and it would be unrealistic to expect a resolution of the conflict in one meeting."

Another source with contacts in the government delegation said the rebel side, made up of four commanders in the Marxist Farabundo Marti National Liberation Front and four political leaders of the Democratic Revolutionary Front, had not focused its attention on specific issues but persisted in raising a wide variety of topics. In addition, he indicated, there were differences over the government's insistence that the meeting focus on a Central American peace plan signed Aug. 7 in Guatemala and the rebels' demands for a wider discussion of a "global political solution."

One factor in the guerrillas' reported reluctance to embrace the regional peace plan is a concern about the "symmetry" it implies between the FMLN and the Nicaraguan rebels known as contras. El Salvador's Marxist rebels reject any comparison with the rightist, U.S.-backed contras, although they are implicitly lumped together in the Guatemala agreement.

The contras have tried to take advantage of the implied symmetry, calling on Nicaragua's government to hold talks with them coinciding with yesterday's meeting here. Unlike the Salvadoran and Guatemalan governments, however, the Sandinistas have refused to consider any talks with their armed opponents.