Opponents in the long-disputed issue of independence for South-West Africa, or Namibia, sat down together at a conference table for the first time here today only to encounter another stumbling block.

United Nations Secretary General Kurt Waldheim, opening the conference designed to bring peace and then independence to the territory, warned of "disastrous consequences" if it fails.

The first working session was tentatively scheduled for Thursday, but Waldheim made it clear to reporters tonight that agreement was still lacking on the status of participants. The issue threatens to scuttle the conference. o

Waldheim said the snag resulted from demands by Namibia's "internal political parties" to speak on their own behalf.

The South-West Africa People's Organization, which the United Nations recognizes as the "sole and authentic representative of the Namibian people," contends the internal parties are "puppets" of South Africa.

South Africa, which administers the mineral-rich former German colony even though its mandate to do so was revoked by the United Nations in 1966, has said it is just an observer at the talks and has threatened to withdraw unless the internal parties are accorded the same status as SWAPO.

Waldheim said he planned a series of meetings Thursday morning in the hope of finding an acceptable formula allowing the internal parties to identify themselves while accepting that they are part of the South African delegation.

The internal parties, chiefly represented by blacks, are avowed enemies of the guerrilla-backed SWAPO.

The seating at the opening session, an intensely touchy subject, placed SWAPO leader Sam Nujoma and 21 colleagues along one side of a square table.

Across from them sat the Namibia delegation headed by the South African administrator general, Danie Hough. He and other delegates from the territory, including Dirk Mudge, white chairman of the Namibia's ministerial council and leader of the governing multiracial Democratic Turnhalle Alliance, occupied the front row facing the SWAPO team. The South Africans sat behind the Namibian delegation.

On the third side sat observers from the front-line states -- Angola, Mozambigue, Zambia, Tanzania, Zimbabwe and Botswana -- from the five Western powers who drew up the U.N.-backed settlement plan -- the United States, Canada, Britain, France and West Germany -- and from Nigeria and the Organization of African Unity.

Waldheim and his aides occupied the fourth side. Waldheim said he planned to extend his stay in Geneva by several days so he could remain "actively involved behind the scenes."

In South Africa yesterday, Foreign Minister R. F. (Pik) Botha said in a radio interview that South Africa would rather face economic sanctions than permit a "terrorist group" to govern Namibia.

Absence of significant progress in Geneva would likely lead to increased calls in the United Nations for sanctions against South Africa.