The South African government said tonight that while it would allow a U.N. envoy to come to Mamibia (Southwest Africa), it reserved the right to decide whether his proposals for implementing a U.N. approved plan for independence in the territory would be acceptable.

In what amounted to a qualified reaccpetance of the Western independence package adopted by the U.N. Security Council last Thursday, South Africa has cleared the way for the initiation of an unprecedented U.N. operation in Africa that will involve 5,000 troops and a civilian task force to oversee elections of about 1,500 civilians.

At the same time, Pretoria has put the spotlight on what is probably the most vulnerable aspect of the Western proposals - whether the United Nations, through its special representative, or South Africa, through its administrator general in the territory, has the last word on how the Western plan is to be implemented. The proposals do not include mechanism to resolve disputes between the two.

Yesterday's announcement, made by Foreign Minister Pik Botha after a five-hour Cabinet meeting, follow several days of implicit threats from South Africa that it might withdraw its acceptance of the Western plan because of Western support last Thursday for another resolution adopted by the United Nations.

That resolution called for steps to be taken for the early "reintegration" of Namibia's only deepwater port, Walvis Bay, into Namibian territory. South Africa claims it has legal sovereignty over Walvis Bay that the United Nations cannot challenge.