Sudan is sending a top-level government delegation to Moscow this week in a bid to enlist Soviet diplomatic support to help end the two-year-old civil war raging in the south.

Headed by Lt. Gen. Taj Eddin Abdullah Fadl, deputy chairman of the ruling Transitional Military Council, the delegation will ask the Kremlin to talk to its Marxist allies in Ethiopia about stopping their aid to the rebels in southern Sudan, according to officials.

Although the Foreign Ministry has favored improving relations with Moscow ever since president Jaafar Nimeri was overthrown last April, the Moscow mission was delayed two months ago at Soviet request and for fear of exacerbating already strained relations with Washington.

Mindful of the need to reassure the Reagan administration, whose aid is considered vital, a Foreign Ministry official said, "Whatever happens with relations with the Soviets, our relations with the West, and especially the United States, will be at a higher level."

The Soviet request for a delay reflected what western diplomats here consider the Kremlin's dilemma: a desire to improve relations with Sudan without endangering ties with Ethiopia, Moscow's staunch ally in the strategic Horn of Africa.

For Gen. Fadl and the civilian ministers traveling to Moscow, the mission marks not just a determination to demonstrate Sudan's new nonaligned stance, but a tacit admission of its failure to negotiate successfully with the Ethiopia-based Sudanese People's Liberation Movement.

Sudanese diplomats described the Moscow mission as a logical step in testing possible Kremlin leverage on Ethiopia, the rebels and such Soviet allies as the Cubans and East Germans, who have been reported to aid the rebels.

Reflecting a growing pessimism, Sudanese officials said they doubted that the Moscow mission would bear fruit before April elections here produce a new government.

The rebels, led by John Garang, an American-educated former colonel, played a major role in weakening Nimeri's erratic 16-year rule.

But to the surprise of Sudanese civilians and military whose opposition brought Nimeri down, Garang has refused to deal with the transitional rulers on the ground that they are the former strongman's heirs.

Sudan's success in persuading Libya to stop aiding the rebellion had raised hopes of a quick end to the war. The new Khartoum authorities assumed that Garang would negotiate a new deal, enshrining democracy and power sharing between the Arab northern majority and the Christian and animist southerners.

Despite a series of talks in Ethiopia last fall between Garang and the National Alliance of Trade Union and Professional Associations, which spearheaded the decisive street demonstrations against Nimeri, no agreement has been reached on meaningful negotiations.

With time running out before the April elections, Sudanese officials reluctantly have concluded that Garang is not a free agent. However, the transitional authorities have refrained from repeating Nimeri's charges that Garang is a Marxist.

Sudanese officials say they have made several unreciprocated efforts to normalize relations with Ethiopia: the dispatch of two military missions to Addis Ababa, the return there of a Sudanese ambassador, an offer to close the common border to anti-Ethiopian rebels in Eritrea and Tigray and the closing of the rebels' political offices in Khartoum.

A diplomat said Ethiopian officials had "said very bluntly they do not think the Sudan can live with the southern rebellion, whereas they are used to Eritrea," where a secessionist struggle is now in its third decade.

The Sudanese war continues to drain the resources of the technically bankrupt government. But despite Garang's threat to carry the war to the north, his only thrusts outside the south have been countered by the Sudanese Army so far.

Against this background, Sudanese officials discounted any major breakthrough this week when Gen. Abdel Rahman Swar-Dahab, chairman of the Transitional Military Council, and Ethiopian leader Lt. Col. Mengistu Haile Mariam met with other regional leaders in neighboring Djibouti.

Mengistu and Somali President Mohammed Siad Barre, longstanding foes in the Horn of Africa, held talks in Djibouti Friday for the first time in a decade, Somali Foreign Ministry sources told Reuter.

They said the two leaders discussed the disputed Ogaden Desert region and two border villages that Somalia says are occupied illegally by Ethiopia.

Official Sudanese thinking about the future is split between those convinced that a popularly elected government stands a better chance of negotiating with Garang and Ethiopia and those who feel that the best chance for a wuick peace lies with the transitional authorities.