State Department officials said yesterday that a major advance had been made in the negotiations to end the 15-year civil war in Namibia and they believe a final agreement could be in hand in three to four weeks.

"Nothing left on Namibia could be defined as a serious enough issue that it, in itself, would jeopardize the negotiations," a State Department official said.

Sam Nujona, leader of the South West Africa People's Organization, denied that partial agreement had been reached, Reuter reported from Paris. "The war for Namibia's independence is continuing," he said.

It was not certain that a consensus had been reached on the sensitive issue of Cuban troops in neighboring Angola. South Africa has demanded that the Cubans and other Soviet Bloc troops be removed from Angola before a settlement can be reached. Guerrillas of the Southwest Africa People's Organization (SWAPO), who are based in Angola, have protested that linkage as a delaying tactic, and all five Western nations involved in the negotiations have not formally recognized it.

The State Department has insisted that the questions are separate. Department officials yesterday would say only that they expect "parallel progress" on the two issues and that the United States has been discussing a "whole range" of questions recently with the Angolans. "The implication there is that we're making progress and moving ahead," one official said.

Negotiators meeting for the past week at the United Nations have "successfully" concluded the first phase of their talks, thus reaching agreement on the volatile issue of setting up an electoral system and the constitutional principles to govern the country, the State Department announced yesterday.

The announcement means that a complicated Western proposal involving both constituency and proportional voting to elect a constitutional assembly for Namibia has been dropped, State Department officials said. That proposal had been bitterly opposed by the SWAPO guerrillas and negotiations had been bogged down for months on the subject.

Instead, the officials said, the negotiators for the five Western nations, the African front-line states, SWAPO and South Africa meeting at the U.N. agreed that the assembly will be elected from single-member districts or by proportional representation. That decision will be made later by the South African administrator-general of the territory and the U.N. official named to monitor the process, U.S. sources explained.

One State Department source who is following the negotiations closely said that no timetable has been established for the completion of the talks but that negotiators believe an agreement could be in hand within three to four weeks. The plan could then be implemented by late summer or early fall, with elections seven months later, he added.

South African diplomats here said that the independence plan could be set in motion by early next month. They said all remaining problems were well on the way to a solution as long as the question of the Cubans continues on the "parallel" track.

The independence of Namibia has become a major international concern and a primary African concern. South Africa has ruled the mineral-rich territory under a 1920 League of Nations mandate that the U.N. revoked in 1966. Independence would transfer the balance of power from 90,000 whites to 1 million blacks.

Officials involved in the negotiations began to express some optimism last fall as U.S. Assistant Secretary of State Chester A. Crocker embarked on a new negotiating method. The talks were broken up into phases, with the first dealing with the constitution and a cease-fire. The second phase deals with the technical details of the cease-fire and implementing the plan.

The five Western powers involved are Canada, Britain, West Germany, France and the United States. The "front-line" African states invited to the talks are Angola, Mozambique, Zimbabwe, Botswana, Tanzania, Zambia and Nigeria.