The withdrawal of a party representing the majority Ovambo tribe from the South African-backed political alliance in Namibia has thrown politics in the territory into confusion.

Peter Kalangula and his National Democratic Party withdrew yesterday from the Democratic Turnhalle Alliance, a grouping of 11 ethnically based parties that South Africa has put in charge of the internal administration of the disputed territory, also known as Southwest Africa.

The departure of Kalangula, the black coleader of the alliance, is a crippling blow to the coalition. The other coleader, Dirk Mudge, is a white politician operating in a predominantly black country, and Kalanguala was the alliance's rising black star.

As a member of the Ovambo tribe, which makes up 46 percent of the population of Namibia, Kalangula represented South Africa's best hope of finding a candidate who could provide a serious challenge in any future elections to the nationalist guerrilla movement, Southwest Africa People's Organization (SWAPO).

Other political leaders in Namibia expressed fears that the breakup of the alliance might cause South Africa to stall on negotiations, spearheaded by the United States, over the future political status of the territory. A key issue in the talks is the holding of elections.

South Africa, which administers Namibia in defiance of U.N. resolutions, is anxious to avoid having to hand it over to SWAPO, which it regards as a Soviet surrogate.

There were indications that Kalangula might try to form a "third force" to participate in an election.

He said today that he wanted other political leaders to join him to form a new national party. Several leaders of parties not involved in the Democratic Turnhalle Alliance expressed cautious interest in his plan. But there are 45 political parties in Namibia, which has a population of less than a million, and each is reluctant to surrender its identity.

The split of the Democratic Turnhalle Alliance grew out of friction between Mudge, its chairman, who is leader of the white party in the alliance, and Kalangula, who was president of the alliance.

The dispute was primarily over Mudge's insistence that the alliance remain based on ethnic parties.

Kalangula took the position that this bears too close a resemblance to South Africa's policy of apartheid, or ethnic separation, and that it would lose the alliance support among blacks in an election fight against SWAPO.

He urged that the alliance become a single, nonethnic party. When it refused he merged his own party with two smaller ones as a step in that direction. This triggered the break.

Expressing fears that this weakening of the Democratic Turnhalle Alliance might cause South Africa to back off the settlement negotiations, Andreas Shipanga, leader of the SWAPO-Democrat Party, said today in a telephone interview from Windhoek, Namibia's capital: "We fear this could have a very negative effect on the negotiations. If it doesn't wreck them altogether, it may cause South Africa to delay to give the DTA time to recover."