JOHANNESBURG, DEC. 30 -- The government of the ostensibly independent tribal "homeland" of Transkei was overthrown in a military coup d'etat today for the second time in three months in a new embarrassment for South Africa's homeland policy of racial separation.

The commander of the Transkei Defense Force, Maj. Gen. Bantu Holomisa, declared on Radio Transkei that he had removed Prime Minister Stella Sigcau, suspended the constitution and imposed martial law on Transkei's 3 million inhabitants because of alleged corruption in the government.

Holomisa told the South African Broadcasting Corp. that Sigcau was "on leave," and that he and a predominantly military junta would rule Transkei temporarily.

Sigcau had been in office only since Oct. 6, two weeks after eight cabinet ministers were forced to resign at gunpoint during a bloodless Army coup that effectively ousted the previous prime minister, George Matanzima, amid allegations that he had accepted a $500,000 kickback on a building contract. Matanzima had left Transkei for South Africa, purportedly for medical care, before the Sept. 24 coup.

For years Transkei has been torn by feuding between Matanzima and his brother, President Kaiser Matanzima, who was banished to a remote area earlier this year after implicating his brother in corruption.

The oldest of four black homelands declared independent by South Africa but not recognized as sovereign by any other country, Transkei has increasingly become a symbol of the failure of Pretoria's homeland policy, the cornerstone of apartheid's grand strategy of separating blacks into tribal areas and giving them their own governments.

Although the South African government pumps about $2 billion a year into the homelands, abject poverty is widespread -- in contrast to the palatial housing for leaders and their relatives and lavish gambling casinos that cater to visiting whites.

For more than a year, Transkei has been in a state of near-war with the neighboring homeland of Ciskei and on several occasions has sent white mercenary soldiers there to attack government installations.

Transkei's bizarre coups and failed cross-border raids have gained its government security forces the sobriquet of "Keistone Kops" among many South Africans.

Telephones in Transkei government offices went unanswered today, and details of the coup were sketchy, but journalists in the homeland reported that there apparently was no violence. The whereabouts of Sigcau, a 50-year-old widow of royal descent who had been minister of posts and telecommunications before being made prime minister, were not known.

Holomisa declared over Radio Transkei that martial law had been imposed "as a result of unavoidable circumstances."

Transkei residents reached by telephone said the government radio was playing martial music and periodically reading Holomisa's declaration. They said Army vehicles with loudspeakers patrolled the streets, announcing the coup d'etat, while helicopters circled overhead.

Roadblocks were reported to have been erected by the Army throughout the 18,000-square-mile enclave, which is on the Indian Ocean coast between the port cities of Durban and East London.

A message from Radio Transkei to the South African Press Association quoted Holomisa as saying that Sigcau had been removed for being "involved in the corruption and bribery which we are fighting and which was practiced by the former ministers that had recently been removed from their posts in an anticorruption purge."

For several months, the Army chiefs have waged a campaign against corruption in Transkei, which a special commission of inquiry recently concluded had cost the homeland about $22 million because of improper actions by George and Kaiser Matanzima.

When she took office in October, Sigcau vowed to combat nepotism and corruption, and South Africa's state radio hailed her as Africa's first woman prime minister.

Holomisa led a group of black Army colonels and majors last April in a purge of white mercenaries, most of them veterans of the Rhodesian war, who had gained virtual control of the Transkei Defense Force.

About 30 of the mercenaries were arrested and expelled amid rumors of an attempted coup. They included Maj. Gen. Roy Reid-Daly, a former commander of the Transkei Army and one-time commander of the elite Selous Scouts of Rhodesia, now Zimbabwe, during that country's war for independence.

Some of the former Selous Scouts were implicated in a spectacular raid on a prison in neighboring Ciskei in September 1986, in which Maj. Gen. Charles Sebe, the brother and political rival of Ciskei President-for-Life Lennox Sebe, was freed and taken to Transkei.

The Scouts also were involved in a machine-gun and mortar attack on Lennox Sebe's palace Feb. 19.