Soviet and Cuban backing for the Southwest Africa People's Organization (SWAPO) and fears of an increasingly authoritarian stance by its president, Sam Nujoma, have caused some uneasiness in the close working relationship between the socialist-inclined movement and influential church leaders here.

Clergymen say they are wary of increasing dependence of the movement on Communist countries that they fear will grow if there is not a speedy and peaceful transition to independence in this territory ruled as Southwest Africa by South Africa for 58 years.

"The longer a settlement is delayed, the more likely SWAPO is to come under the influence of the Eastern bloc," said Justin Ellis, the former director of Namibia's ecumenical Christian Center. Ellis recently was deported from Namibia by the South African government for his protests against alleged police torture of political prisoners.

With Cuban, Soviet and East German assistance, SWAPO is fighting a guerrilla war against South African troops stationed in Namibia. The United States and four of its allies seek South African cooperation in a plan for United Nations-supervised elections to defuse this war.

Most black Namibian church leaders have given their support to the U.N. plan. The political sympathy of church leaders is extremely important in Namibia which, although its population is less than a million, has one of Africa's highest percentages of Christians. Church leaders here say it is in the range of 80 to 90 percent, with Tanzania the next highest at 65 percent.

Communist backing does "create problems for the church," sais Lukas DeVries, head of the Evangelical Lutheran Church, which has 132,000 black members. "But we say we understand that the SWAPO leaders, after pleading with the Western powers, have had to go to the East."

Last February, the Lutheran church leaders sent a pastoral letter to their congregations warning their "brothers" in SWAPO of the "danger" of the encroachment of Marxisn. According to one informed source, SWAPO representatives at the United Nations were annoyed by the letter.

In the last three years the propaganda of SWAPO has become more militantly Marxist, but there is no evidence that SWAPO would set up a hard-line Marxist state like those in Angola and Mozambique. The exact kind of socialist state it would establish if it came to power is still not clear.

Some church leaders also say they are disconcerted by remarks of Nujoma that SWAPO is not fighting for majority rule in Namibia and by reports that the SWAPO leadership under Nujoma has become more dictatorial, with dissidents imprisoned in cmaps in Zambia.

"We are a little worried when Nujoma says he is not aiming for a democracy because we do not want to come form one dictatorship to another," De Vries said.

An estrangrment between SWAPO and the churches would be in the interest in SWAPO's principle political rival, a South African-backed coalition of parties called the Democratic Turnhalle Alliance. It describes SWAPO as dedicated to godless Marxism and manipulated by the Soviets.

"We hear this propaganda every day on the radio. The government is trying to make people hate SWAPO," said Bishop Leonard Nangola Auala, shose 270,000-member Evangelical Lutheran Ovambo-Kavanga Church operates in northern Namibia in the war zone.But "we cannot hate our church members," he added.

The unusually close working relationship between SWAPO and the churches grew out of their common struggle against South African rule in Namibia.

The SWAPO-church convergence intensified in the early 1970s when both De Vries' and Auala's Lutheran churches, which together represent more than half the black Namibian population, became independent of their white "mother" churches.

De Vries, one of the foremost black theologians in southern Africa, explained how black church leaders refused to accept some missionaries' teaching that the state always had to be obeyed and that the spiritual and political lives of man must be kept separate.

Once the black churches took the attitude that they had a duty to tell the government how it erred, they "gained the confidence of the political movements and, instead of people leaving church, they began to come," De Vries said.

This has led to confrontation with the South African authorities and church leaders are still a target for police harassment. Auala's mission station in Ovamboland, which is the heartland of the guerrilla war, is visited regularly by security police, the bishop said. In addition to Ellis, two other white clergymen, Anglican Vicar General Ed Morrow and a Catholic priest, Heinz Hunke, were deported last year.