Negotiations aimed at reaching agreement on Namibian independence are under way again after more than two years of deadlock over a joint demand by the United States and South Africa that approximately 25,000 Cuban troops be removed from neighboring Angola before the disputed territory can become independent.

After two days of secretive discussions with the South African government, U.S. Assistant Secretary of State Chester A. Crocker left Pretoria tonight with a South African counterproposal to a recent offer by Angola to remove some of the Cubans.

The Cuban government, meanwhile, has given its "total support" to this offer by Angola's president, Jose Eduardo dos Santos, the newspaper Granma, official organ of the Cuban Communist Party, reported yesterday.

According to Granma, dos Santos has proposed the signing of a four-party agreement by Angola, South Africa, Cuba and the Namibian independence movement, the South-West Africa People's Organization, setting out the conditions for this partial Cuban withdrawal.

A brief joint statement issued at the close of the talks in Pretoria today said that the United States would convey South Africa's response to the Angolan offer "as soon as possible," after which further talks between the U.S. mediators and South Africa were expected.

"It is also possible that trilateral discussions between South Africa, the U.S. and Angola could follow," the joint statement added.

Neither Angola's offer nor South Africa's response has been officially disclosed, but according to the Granma report, dos Santos has said that the withdrawal of the Cubans can begin after South Africa has allowed a United Nations-approved process toward Namibian independence to begin, a U.N. supervisory force has arrived in the territory and South Africa has reduced its military presence in Namibia to 1,500, as specified in the U.N. formula.

Dos Santos also has made it a condition of the partial Cuban withdrawal that South Africa cut off all aid to Jonas Savimbi's insurgent National Union for the Total Independence of Angola (UNITA), Granma reported.

According to well-placed diplomatic sources in Pretoria, the Angolan offer is to withdraw altogether two-thirds of the estimated 25,000 Cuban forces. Those remaining would be withdrawn north of the 16th Parallel and concentrated around the capital of Luanda and the oil-rich enclave of Cabinda, which protrudes into Zaire in the far north of the country.

According to these sources, South Africa has conditionally rejected the Angolan offer but made a counterproposal that is expected to lead to a resumption of negotiations.

This indicates that both sides have given ground in a series of U.S.-brokered exchanges that began three months ago.

Angola, which first refused to accept the principle of "linkage," as the precondition concerning the Cuban forces is called, is now apparently ready to remove at least some of the Cubans as part of a package deal.

For its part, South Africa, which first demanded the withdrawal of all Cubans as a precondition for Namibian independence, now seems prepared to accept that a force of less than 3,000 or 4,000 might remain.

Foreign Minister R.F. (Pik) Botha dropped a hint of this during the first day of his talks with Crocker here yesterday, when he told reporters that his government could not "accept the permanent presence of foreign troops in large numbers within our region."

Asked what he meant by "large numbers," Botha replied: "A large number would be a number that constitutes a threat, anything from 3,000 to 4,000 upward."

According to news agency dispatches from Havana, the Cuban newspaper said dos Santos had revealed the outlines of his offer to a closed session of the Organization of African Unity summit that ended in Addis Ababa, Ethiopia, yesterday.

Dos Santos told the African grouping that this program reflected "greater flexibility" by his government than previous conditions it had set for the withdrawal of the Cuban troops.

It is likely that South Africa will also resist the demand that it abandon Savimbi and his UNITA movement. It is expected to try instead to bargain for Savimbi's inclusion in an Angolan government of national unity as part of the package deal.

At a press conference at his headquaters at Jamba, in southeastern Angola, last weekend Savimbi made a bid for inclusion in the negotiations by threatening to launch a major new guerrilla offensive against Luanda if he was excluded.