A South African medical orderly working with Jonas Savimbi's rebel forces inside Angola was killed last weekend by Angolan troops, the South African military announced tonight.

The announcement underlined the continued involvement of South African soldiers with Savimbi's National Union for the Total Independence of Angola (UNITA) despite South Africa's public assertions that it does not support the rebels in their war against Angola's Marxist government.

Gen. Constand Viljoen, chief of the South African Defense Force, said the orderly, a 22-year-old lance corporal, was killed at an undisclosed location during a skirmish between Angolan and UNITA forces. He said it was believed the body was taken to the Angolan capital of Luanda.

A military spokesman stressed the incident was not related to yesterday's invasion of southern Angola by South African forces seeking to destroy bases there of another guerrilla force, the South-West Africa Peoples Organization (SWAPO). The South Africans claimed SWAPO guerrillas were preparing to launch new attacks from their Angolan bases into neighboring Namibia, which is controlled by South Africa.

But the disclosure of the casualty with UNITA has set off renewed speculation that one possible reason for the invasion was to relieve pressure on Savimbi's forces after a major offensive by Angolan troops, backed by Cuban and Soviet military advisers.

Viljoen explained the presence of the orderly and other medical personnel with UNITA in Angola by saying that requests for "humanitarian aid" were considered "on merit."

Military spokesmen in Windhoek, the Namibian capital, said earlier today that SWAPO rebels had killed one civilian and abducted several others in raids inside northern Namibia during the past nine days. The incidents were cited by the government as further justification for the new incursion.

The state-run South African national radio network criticized in an editorial for broadcast Wednesday the State Department's expression of "deep concern" over the invasion in terms that reflected the growing differences between Pretoria and Washington over how to deal with domestic unrest inside South Africa as well as the SWAPO guerrilla threat.

The radio network, whose views usually reflect government thinking, said, "Whether the destroyers are bush terrorists or urban radicals . . . they have to be answered on their own terms. There is no alternative, except surrender to the revolutionaries."

It said the Reagan administration "seems no longer prepared to maintain a fair and evenhanded stance" in criticizing South African military action against SWAPO and police action against urban unrest domestically.

In another regional matter, South African Foreign Minister Roelof F. Botha confirmed he visited Maputo yesterday for talks with Mozambican President Samora Machel concerning allegations that South Africa has "repeatedly" violated the Nkomati nonaggression accord between the two countries.

Botha said his government would investigate the allegations of continued South African military support for Mozambican rebels fighting Machel's government.