The Sudanese government is pressing its investigation into the role of Israel and the U.S. Central Intelligence Agency in the secret airlift of thousands of Ethiopian Jews to Israel late last year and early this year.

But that effort could greatly complicate current emergency relief efforts by the United States for this starving country.

"They've been warned," said one well-informed western diplomat. By publicly emphasizing the role of the United States and exposing CIA personnel, Sudan "may alienate Congress and make things that much more difficult," he said.

Sudan depends on the United States for most of the food now being used to feed its famine-stricken western provinces and for extensive military and economic aid.

But for the new Sudanese government the investigation into the airlift of the Falasha, as the Ethiopian Jews are called, has become the central element in its prosecution of exiled former leader Jafaar Nimeri and members of his government.

Nimeri, who was overthrown April 6, was considered a vital supporter of U.S. interests in the region through much of his 16-year-rule.

The new Sudanese leaders deny that there is any anti-Americanism involved in their prosecution of the case and often acknowledge the vital need for continued U.S. assistance.

No one suggests that Washington has been threatening or attempting to apply direct pressure to stop the case.

Gen. Abdel Rahman Swar Dahab, president of the Transitional Military Council that replaced Nimeri, said in an interview this week that U.S. Ambassador Hume Horan had "emphasized" the "humanitarian" motives for the Falasha operation.

What Israel called "Operation Moses" is viewed widely in the United States and Europe as a heroic effort to save at least one group among the hundreds of thousands of refugees and Sudanese who have been starving here in recent years.

But the new Sudanese government considers officials of the Nimeri regime involved in the Falasha evacuation to have "given aid to the enemy." Swar Dahab said that Israel "is still the enemy." The charge against Nimeri and the others is high treason.

Between 10,000 and 12,000 Falashas are reported to have been relocated to Israel.

The Falashas, widely believed to be members of a small "lost" Jewish tribe, had lived for centuries in Ethiopia. Early in 1984, when famine struck Ethiopia, thousands of Falashas marched to Sudanese refugee camps.

The details of the case, as outlined by investigators and Attorney General Omer Abdelati involve extensive payoffs to Sudanese officials by U.S. and Israeli intelligence services. The largest single payment was said to have been $2 million, paid by "Zionist organizations in Geneva" to a London bank account.

"We are not trying the United States," said Abdelati. "We are trying the vice presdient of this country for many crimes, one of which is that he helped smuggle these Falashas out of this country to Israel, when we are officially at war with that country. And he got paid for it. Abdelati added, "We don't care if these people take the Falashas to Israel. But not through our land. Not by bribing our president."

Abdelati, a softspoken, scholarly leader of the lawyers' union that was instrumental in the series of protests that brought Nimeri down, said, "We feel we've been fooled. Nobody likes that. We feel we have been fooled by a foreign nation, and we have been betrayed by our presdient."

As Kamal Gizouli, a member of the investigating committee put it, "We came to discover that this country was governed by the CIA."

According to Gizouli, the Americans who put the operation together, dealt directly with Oman Tayeb, former first vice president and state security chief, whose security forces were widely despised and were disbanded after Nimeri's overthrow.

Gizouli said that the committee has a report that CIA Director William Casey called Tayeb in February 1985 to discuss the Falasha situation. Tayeb subsequently traveled to Washington for further talks with U.S. officials, and the final Falasha operation was arranged when Vice President Bush visited here and talked with Nimeri at the beginning of March.

According to investigators, Tayeb, who is now in Kuber Prison, has denied any knowledge of the Falasha case until he read news accounts of it in January.

For all the allegations of bribes, Gizouli and Abdelati appeared reluctant to provide documentary evidence. The one example of CIA money being paid out that was cited was about $12,800 for the rental of buses to bring the Falashas to Khartoum in the first airlift and a subsequent purchase of four Nissan trucks in Saudi Arabia by Jerry Weaver, then refugee coordinator of the U.S. Embassy. The trucks were said to have been handed over to state security when the operation was finished.

According to Gizouli, the evacuation of the Falashas appears to have begun in 1981, although U.S. involvement seems to have centered on two airlift operations at the end of 1984 and in March 1985.

Early in the operation a company called Navco leased a small village, Aruz, on the Red Sea coast of Sudan for "touristic development."

Navco paid $320,000 for a three-year contract signed by Tourism Minister Mohamed Majoub. The minister was arrested yesterday.

But according to Gizouli, Navco was a front organization for the Falasha operation.

"Nobody knew what they were doing there," Gizouli said. "And soon after the blowup in the Sudan . . . they disappeared. The whole staff. The directors. They just disappeared. . . ."

Gizouli said police in the area reported that the Navco staff had been flown out in a C130 Hercules transport plane.

Gizouli said the investigators believe Navco was a front for the CIA. But an Eritrean exile in Washington who worked with the operation in its early stages identified Navco as an Israeli cover.

Both Abdelati and Gizouli identified Weaver as a central figure in the operation. Both said they believe that Weaver was a CIA officer. But one foreign diplomat in a position to know said that Weaver was not.

Weaver, who discussed his activities in Sudan for publication and in great detail with a Los Angeles Times correspondent before leaving the country, has strongly denied that he worked for the CIA. In Washington, an authoritative government source also said the allegation that Weaver worked for the CIA was false.

Weaver, according to friends, left the country before Nimeri was overthrown and has not returned.

By Gizouli's account the first airlift, involving 28 flights, started Nov. 21, 1984, and ended Jan. 4, 1985, after the publication of reports about them.

"These people from the American embassy, in coordination with the head of security, Tayeb, brought thousands of the Falashas from Gedaref [refugee camp] to Khartoum airport and then to Israel through some European capitals: Athens, Brussels and Rome," said Gizouli.

"They used chartered air buses through a contract with TEA Co., Trans European Airlines, a Belgian company," he said. European relief officials here confirmed this.

The second airlift took place in March, Gizouli said, after Bush's visit. Bush "organized the whole thing with ex-president Nimeri, who gave the orders to Tayeb."

"The American Air Force got involved," Gizouli said, "using six of their C130 Hercules planes to take out the Falashas with the cover of bringing in some aid."