Western negotiators say they fear that a major South African military incursion begun two months ago deep inside Angola could jeopardize the chances of persuading Angola to remove the estimated 20,000 Cuban troops in that country.

South Africa has insisted on Cuban withdrawal as part of a settlement leading to independence in Namibia, where it has been fighting a war against nationalist guerrillas of the Southwest Africa People's Organization for 15 years.

The protracted negotiations on Namibia are at a delicate stage, as members of the Western negotiating team headed by the United States have been directing an intense series of talks in New York. Agreement has been reached on the first phase of the plan to write a Namibian constitution and elect a democratic government.

Maj. Gen. Charles Lloyd, commander of the South African forces in Namibia, revealed at a briefing for local editors in the territory's capital of Windhoek Thursday that his troops invaded Angola, in pursuit of SWAPO guerrillas, two months ago and are still there. Although South African officials refuse to release many details about the invasion, Lloyd said the troops penetrated 175 miles into Angola to Tecamutete, near Cassinga. He announced that the troops will stay in Angola until a cease-fire is reached.

In that briefing, the first action mentioned by Lloyd was July 16, when South African forces attacked SWAPO bases at Evale and Ionde, about 75 miles inside Angola. But defense officials said later that the operation began June 11.

Lloyd said the incursion was aimed at SWAPO, and the troops had no encounters with Angolan troops or Cubans.

However, he also revealed in an interview Friday that South Africa was deploying Mirage F1 jet fighters over Angola to counter Angola's Soviet-built Mig 23s, which he said had been moved near the operational area. Although the South Africans are known to have placed Mirages in the area before, they never have publicized such moves.

The Angolan Migs are piloted by Cubans, raising the risk of a direct clash between South Africans and Cubans, which could further jeopardize the negotiations. Angola has said that the Cuban presence is justified by continued military threats to its territory from South Africa.

What exasperates the Western negotiators, informed sources said, is that South Africa has made the Cuban withdrawal a condition for a Namibian settlement, yet now its own actions are making that more difficult to achieve.

"It is a difficult enough task as it is, but this action is not best suited to persuading the Angolans that now is the time to get rid of the Cubans," remarked one Western diplomat.

Angola has objected to the Cuban issue being linked to a Namibian settlement, arguing that it is a bilateral matter with Cuba.

South African defense spokesmen refused to speculate on the dangers of their operation sabotaging efforts to negotiate a Cuban withdrawal.

"It is the continued activities of SWAPO that are jeopardizing a cease-fire," said chief press spokesman Brig. Kobus Bosman.

Complicating the Namibia negotiations is the Angolan fear of the guerrilla forces of Jonas Savimbi's rebel UNITA movement, who occupy large tracts of southern Angola.

If the Cubans are withdrawn, Angola believes it will be more vulnerable to Savimbi's thrusts north.

Although South Africa denies aiding Savimbi, it is known to give him considerable logistical support, and the South African raids into Angola are at least partially designed to open the way for UNITA to move in behind the invading troops.

South African raids into Angola are frequent, but the government often does not disclose details of the operations. This latest raid is believed to be the largest since a move last August, in which the South Africans claimed to kill more than 1,000 SWAPO guerrillas in one week. The Angolans reported then that most of the dead were unarmed refugees.

The South Africans also moved into Angola in late November for 18 days and reported killing 71 insurgents. The South Africans then conducted raids penetrating about 160 miles into the country.

A defense statement Friday said 418 SWAPO insurgents had been killed in the latest invasion and 16 South Africans had died.

Despite the scope of the operation, it appears to have been cloaked in secrecy, and Angola did not report the invasion. Bosman said that the loss of a helicopter and 15 men last Monday made an announcement necessary, but it was not until Lloyd's briefing that the scale of the operation became known.

The fighting is taking place in a very remote bush country, which is thinly populated, and communications are scarce. Some observers also said that the South African involvement may not have been realized at first, and the operations may have been credited to Savimbi's troops.

Informed sources said it is still uncertain why the South Africans staged a major confrontation now during the delicate negotiations. Lloyd said in his Windhoek briefing that the defense force received information that SWAPO had established advance headquarters near Evale and Ionde, but when his troops reached there the bases were deserted. The South Africans continued to move north, Lloyd said.

They finally caught up with the SWAPO group at Tecamutete Aug. 10, killing 118 of them, he explained.

Bosman said the operation stemmed from the discovery of SWAPO documents ordering the assassination of political leaders in Namibia and the caching of arms near the Namibian border prior to an anticipated cease-fire. "Our forces went in on the basis of that information, then received follow-up information, which took them further," Bosman said. "It was not planned in advance as a major operation."