Cuban troops are now fighting in Ethiopia against secessionist forces in the province of Eritrea, a new Cuban military role following their use in the Ethiopian-Somali conflict, a White House official said yesterday.

At the same time, the White House has increased its estimate of the number of Cubans presently in Ethiopia to 16,000 or 17,000. This compares with the last U.S. estimate of 13,000 Cubans, most of them combat troops, in that African nation.

This information was given to reporters by an official aboard President Carter's plane en route to Lagos, Nigeria. The precarious situation in the Horn of Africa, where American and Soviet strategic interests are in conflict, is one of the subjects on the agenda of Carter's talks in Nigeria.

One of the important international questions since the end of large-scale fighting early last month between Ethiopia and Somalia in the Ogaden region of Ethiopia has been whether Cuban troops, which supported Ethiopia in that war, would be shifted to Ethiopia's internal conflict in Eritrea.

"Small scale units" of Cubans are now being deployed in Ethiopia's northeast province of Eritrea, reporters abroad the president's plane were told.

"There is some indication that they will be massively deployed, although it isn't conclusive yet," said the senior official who declined to be identified by name. He said that "the fact that the inflow" of Cubans into Ethiopia "has continued, at least opens up that possibility."

In addition to the Cuban combat forces, the Soviet Union has had an estimated 1,000 military advisers supporting Ethiopia in its war with Somalia, fighting in the name of repelling Somalian "aggression" into Ethiopia.

The use of Cuban troops in the 16-year-old Eritrean "liberation war" has considerably different implications than their use against the Somalis.

Many of the forces fighting for the independence of Eritrea, a former Italian colony, are Marxists, supported by Marxist nations and urged on in the past by Cuba, among other nations. The war in Eritrea is clearly a civil war with outside support.

President Carter said on March 17 that the Soviet military intervention "in local conflicts" along with "mercenaries from other Communist countries" - meaning Cuba - is "an ominous" development.

The State Department issued its own new estimate of Cuba in Ethiopia earlier yesterday, saying the figure was "at least 15,000".

Department spokesman John H. Trattner said the new figure was based on improved intelligence and did not necessarily represent new Cuban reinforcements just sent into Cuba.

The higher figure from the White House party later in the day showed that once again the White House and State Departments were at odds on their numbers with the White House publicizing the upper level of an estimate and the State Department the lower level.

But yesterday, in addition, the State Department spokesman was saying that there was "no evidence that Cuban forces were engaged in Eritrea" while the White House was saying just the opposite. No one offered to clarify that discrepancy, although the State department spokesman inevitably deferred to the higher authority.

Many diplomats had thought it improbable that Cuba would want to entangle itself militarily in Eritrea, although Cuban military advisers for some time have been reported aiding Ethiopian government forces in the province.

As early as last mont the Eritrean People's Liberation Front announced that 2,000 Cubans had flown to Asmara, the capital of Eritrea, from Angola, the original site of major Cuban military involvement in Africa.

Until yesterday, however, American officials had said they had no confirmation of Cuban military units in Eritrea.

President Carter early last month publicly urged Somali President Mohammed Siad Barre to withdraw his troops from Ethiopia where they were fighting in the name of "liberating" ethnic Somali peoples from Ethiopian rule so as to remove any justification for a Soviet-Cuban combat presence in Ethiopia.

Siad Barre simultaneously announced a troop withdrawal, last month, although by that point his forces were being routed by the Ethiopians reinforced with the Cuban troops.

The Western Somali Liberation Front, however, backed by Siad Barre's government, has said it is determined to fight on.

On Thursday a communique said the Front ambushed a troop convoy in the center of the Ogaden and killed nine Cubans and 170 Ethiopian soldiers, Somali's official radio annouced.

In turn, Somalia claimed yesterday that two Soviet-built Mig-21s, which presumably would be from Ethiopia, carried out two bombing raids on the Somali village of Kalabaid, west of the northern regional capital of Hargeisa.

This was the first time Somalia has claimed such an attack since its regular troops withdrew from the Ogaden.

Ethiopia clearly imlied yesterday that its Cuba-backed troops might invade Somalia if ethnic Somali guerrillas continue their hit-and-run war in the Ogaden desert.

A broadcast by Addis Ababa Radio said that while the Ethiopian government has "firmly told the work community that it has no wish to violate Somalia's territorial integrity . . .

The Somali leadership has continued its policy of invasion and expansionism and has declared a genocidal war. The Ethiopian people will no longer accept this.

"Although Ethiopia does not want war, in accordance with international law it will be compelled to safeguard its rights in the face of future attacks. This is what Ethiopia wants to make clear."