Eritrean separatists have rejected a Soviet proposal for a federation to end the civil war in Eritrea, Ethiopia'a northernmost province, and have signed a unity pact to end a schism that has bedeviled their movements for the past six years, according to Eritrean sources here.

The Eritrean rejection of Moscow's mediation efforts represents the second setback to Soviet diplomacy in this explosive region in the past few months, In mid-March, the Soviet Union and Cuba tried unsuccessfully to resolve the burning territorial dispute between Somalia and Ethiopa, forcing a secret meeting between Somali President Mohamed Siad Barre and the Ethiopian military strongman Lt. Col. Mengistu Haile Mariam in the South Yemen capital Aden.

The Soviet initiative over Eritrea comes in the wake of Moscow's decision to replace the United States as Ethiopia's main arms supplier while remaining Somalia's main foreign backer.

It is likely Moscow is now beginning to realize just how diffullt it will be to straddle all the conflicts in this corner of Africa and remain on good terms with all the feuding parties.

So far, there is no indications that either the Eritreans, the Ethiopians or the Somalis, despite their common Marxist-orientation, are willing to compromise over what each regards as a vital national interest and to accept Soviet and Cuban mediation.

A number of Arab countries, including Sudan, have attempted to mediate between the Eritrans and the Ethiopia but these efforts have also failed.

The Soviets reportedly, made contracts with leaders of the three Eritrean factions here, in South Yemen and Somalia. Eritrean representatives first met with Soviet diplomats in the Yugoslav embassay here in Khartoum.

According to Osman Saleh Sabbe, leader of one of the factions, the Soviets proposed a federation with Ethiopia that would give "recognition of a distinctive Eritrean status."

The Soviet proposal was rejected, he said. Other Eritrean sources here confirmed that all three factions decided independtly to refuse outright any solution short of total independence for the former Italian colony and were committed to fighting until the Ethiopian government agrees to this.

Ethiopia is currently forming a "peasant army" of 50,000 to 100,000 soldiers for waht may well be a final attempt to hold on to the province.The Eritreans control virtually all of the countryside and have recently taken over a number of small and medium-size towns.

So far, the peasant army has not begun its march into Eritrea, although the Ethiopian army has been reinforcing its 25,000-man force there with mewly trained troops. Western diplomatic sources in Somalia have said 50 Cuban military advisers have arrived in Ethiopia, presumably to train the peasant army. Some 400 to 500 more are expected in the near future.

The Eritreans say the immediate Ethiopia objective is to sweep their guerilla forces from the highland area of the province and then, with Cuban and oviet backing, to open negotiations for a political solution, bargaining from an improved military position.

If the peasant army falls to crush the Eritrean guerrilla forces, however, it appears highly likely the Ethiopians will lose control of the province.

Meanwhile, the two main factions of the Eritrean nationalist movement, the Eritrean Liberation Front Revolutionary Council and the Eritrean People's Liberation Front have signed a five-point agreement pointing toward the reunification of all Eritrean guerilla and political forces.

The accord, signed May 31, basically sets forth a procedure for bringing about reunification of all factions and pledges the two main ones to work together to thwart the coming Ethiopian offensive.

The Eritrean Liberation Front was given the responsibility of bringing about a merger between it and the faction led by Saleh Sabe, who broke off last year from the People's Front and has become a major divisive issue in the Eritrean movement. He has strong outside backing, particularly from Iraq, but relatively few guerillas.

The two main factions are at odds, partly because of the conflicting personalities of their leaders and partly over their different approaches toward how to flight the war and organize their followers. Both have now agreed to establish a joint National Democratic Front until independence is achieved. No date for the complete merger of all factions was set.

The prevailing impression among observers here is that the latest agreement, the second in the past two years, represents some progress on reunification of the Eritrean movement but until full accord on how or when to merge totally is reached, the possibility of a bloody power struggle among Eritrean factions cannot be excluded if independence comes.