Long-running negotiations about the future of Namibia have reached a crucial stage following a letter from President Reagan to several African leaders suggesting that removal of Cuban troops from Angola might help lead to Namibian independence.

Sources here and in New York confirmed existence of the letter last week after the African leaders, in a little-noticed communique following a meeting in Lusaka, Zambia, referred to a "new element [that] has been introduced by the United States which attempts to link the negotiations for independence of Namibia with the withdrawal of Cuban troops from Angola."

Leaders of the "front-line states" rejected any specific linkage between the two issues in their communique, but administration sources noted that the statement left the decision on the future of the Cuban forces to the Angolans. Deputy Assistant Secretary of State Frank Wisner is planning a trip to Luanda, the Angolan capital, perhaps this week and is expected to focus on the issue.

Wisner, along with Ambassador Vernon Walters, has been the key U.S. negotiator with the Angolans in meetings throughout the summer while other aspects of a Namibia settlement have been handled through contacts at the United Nations and in other forums between representatives of five Western nations, South Africa and the front-line states.

Namibia, the focus of the Reagan administration's Africa policy, has been a preoccupation of Chester A. Crocker, assistant secretary of state for African affairs.

The Reagan letter, according to the sources, was part of an effort to persuade several African officials who have taken the lead on Namibia that an independent Namibia is near only if the Cuban troops barrier can be hurdled. The officials represent nations such as Zambia, Mozambique, Zimbabwe, Botswana and Tanzania.

Diplomatic sources say it is unclear what advice the African leaders might have given the Angolans privately on the issue, which is highly contentious among countries on the dividing line between black and white-ruled Africa.

Administration spokesmen spoke optimistically on Namibia as recently as mid-July, but tension increased as South African forces launched another major incursion into Angola aimed at guerrillas of Southwest Africa People's Organization (SWAPO).

The South Africans have begun to pull back to their bases in Namibia, and some troops have been sent home, sources said.

South Africa is sending a special mission to the United Nations this week that is expected to respond on what is said to be the last issue in the proposed settlement agreement -- the method of electing the constituent assembly to write a constitution for an independent Namibia.

About 1 million people live in the 310,000 square miles that make up Namibia, or South-West Africa as it was known after its colonization by Germany in the 19th century. South Africa received a League of Nations mandate for the territory after World War I and has continued to rule it in defiance of the United Nations.

Following the independence of Zimbabwe in April, 1980, the focus of southern Africa politics shifted to Namibia and its volatile mix of diamond, zinc, copper and uranium wealth, guerrilla warfare, South African interests and the 15,000 to 20,000 Cuban troops in neighboring Angola.

Angola has insisted that it will not ask Cuban troops to leave until it is assured about Angola's territorial integrity, believed to be a reference to South African raids in southern Angola and continuing outside support for the guerrilla forces of Jonas Savimbi.

South Africa cites its own security considerations and says it will not consider pulling out of Namibia until Cubans leave Angola.

Other U.S. observers of the delicate negotiations say there is also concern about possible South African wavering.

South African Prime Minister P. W. Botha is besieged by his arch-conservative right wing, and there are fears that Pretoria may "become scared of its own courage" as the moment for commitment to a settlement nears, in the words of one observer.

Should a parallel agreement on the future of Cuban troops be reached, an immediate pullout is unlikely, according to sources. Withdrawals likely would come only at the actual declaration of an independent Namibia, which could come many months after all parties have agreed to begin the process.

Congressional sources also say Angola is insisting on maintaining a Cuban military training team and a large number of civilian technicians in the country.