President Samora Machel of Mozambique snubbed President Reagan's top adviser on Africa today, registering the clearest disagreement yet from any African country over the direction it perceives in the new administration's policy toward the continent.

Another setback for Reagan's southern Africa policy came almost simultaneously, when U.S. officials in Pretoria announced that the presidential adviser, Chester Crocker, assistant secretary of state-designate for African affairs, would also not be given an expected meeting with South African Prime Minister Pieter W. Botha.

Botha's decision not to meet Crocker appeared to indicate displeasure with the administration's Africa policy from another direction. While Mozambique and other black African nations are upset over what they see as an administration tilt toward South Africa, Pretoria reportedly is upset about comments Crocker has made so far on his trip denying such a tilt.

A grim-faced Crocker left here for Pretoria, with a short stopover in Swaziland, shortly after a 75-minute meeting with Foreign Minister Joaquim Chissano that the Mozambican official described as "not pleasant."

Sources familiar with the two sides said both Chissano and Crocker became "angry" when the talks shifted to bilateral relations. Relations have been strained since last month when the leftist government of Mozambique expelled four American diplomats for alleged spying activities and the United States retaliated by suspending food aid.

In his previous four stops to consult with African nations about the Reagan administration's policies toward Africa, Crocker had routinely seen the heads of government in Kenya, Tanzania, Zambia and Zimbabwe. The United States has closer relations with these four countries.

Chissano said in an interview with The Washington Post that there were significant differences between the United States and Mozambique over policies toward South Africa and Namibia, the territory Pretoria illegally controls as South-West Africa. He described the overall talks on southern Africa as "not bad."

[At the United Nations, five Western countries announced today that they would meet in London next week to work on new proposals for the independence of Namibia on the basis of talks conducted in Africa by Crocker, The Associated Press reported.]

Crocker said the United States favors a constitutional conference involving all sides in the Namibia dispute before independent elections, according to the foreign minister.

"We are not of the same opinion," Chissano said, adding that most of black Africa would also oppose such a solution.

The U.S. proposal would involve a change in the plans drawn by the United States, Britain, France, West Germany and Canada for a U.N.-supervised election for a constituent assembly leading to independence. uThe South West Africa People's Organization, which is fighting a guerrilla war for independence, and South Africa have accepted the Western plan in principal but South Africa has refused to implement it.

"Only the Namibian people can discuss the constitution," Chissano said.

Crocker is bound to run into trouble on this issue again later in the week when he visits Angola, with which the United States has no diplomatic relations. It was announced today that the six "front-line" state involved in the Namibia negotiations -- Angola, Mozambique, Zambia, Zimbabwe, Tanzania and Botswana -- will have a summit meeting in Luanda, Angola, Wednesday. Namibia and Crocker's tour of Africa are believed to be on the agenda.

Chissano also said there are "big differences between our views and Reagan's on South Africa. The administration has talked of significant changes in the country's system of racial separation called apartheid.

"We feel the changes in South Africa are not significant at all," the foreign minister said. "The changes are aimed at protecting apartheid."

Chissano said he concluded from Crocker's remarks in the meeting that "the American government wants us to apologize for having expelled the CIA spies. We are not prepared to apologize for being spied on by the CIA. We would not tolerate any interference in our internal affairs."

Commenting on the failure of the Crocker delegation to have a meeting with Machel, the foreign minister said, "If they had presented their questions [to Machel] in the way they presented them to me, it would have been a worse result." Chissano said the Americans had asked for a meeting with the Marxist leader before their arrival but were told that such a session "was not forseen."

Machel was the first African leader to criticize what black Africa sees as Reagan's tilt toward white-ruled South Africa.

Before Crocker's arrival yesterday, there had been a slight upbeat note since Mozambique last Friday released the last of two American civilians jailed at the time of the expulsion of the diplomats.

Crocker is scheduled to meet Wednesday with Foreign Minister Pik Botha and their talks are expected to center on ways to reactivate negotiations on a peace settlement in Namibia.