Orlando Cristina, reportedly the secretary general and second in command of the rebel Mozambique National Resistance Movement, has been shot dead in South Africa, police confirmed today. There was no indication who killed him.

According to sources in the Portuguese community here, Cristina's body was found Sunday in a farmhouse north of Pretoria, where he was thought to have been living. He had been shot in the neck while in bed, the sources said.

The disclosure that Cristina was in South Africa is expected to give fresh impetus to Mozambican accusations that the Pretoria government is aiding the rebels, who have been causing widespread disruption in the radical black republic on South Africa's eastern border.

It is also likely to revive accusations by blacks that South Africa is trying to destabilize neighboring black states in retaliation for their criticism of its own system of strict segregation and white minority rule.

The South African government repeatedly has denied that it is following a policy of destabilization, accusing its black neighbors in turn of trying to divert attention from their own inability to control growing internal dissension.

Blacks cite the disclosure that four soldiers killed inside Zimbabwe on Aug. 18 were members of the South African Army who had crossed the border in a group and been engaged by a Zimbabwean Army patrol.

South Africa's Army chief, Gen. Constand Viljoen, said at the time that the men had gone on an unauthorized mission to release a friend they thought was being held in Zimbabwe.

Then the London Observer said in February that a man who had been killed while trying to sabotage a railroad track in Mozambique was a man from Northern Ireland named Alan Gingles who was serving in the South African Army.

Questioned about this in Parliament, Defense Minister Mangus Malan confirmed that Gingles was in the South African Army but refused to give any other information about him or how he died.

It had long been rumored here that Cristina was living underground in South Africa, but there was never any confirmation.

The government is still saying little about him. The police statement, issued by Col. Chris Coetzee, head of the media liaison division, after repeated press inquiries, said only: "The police are investigating a shooting incident in which a white man, Orlando Cristina, was killed in the Pretoria area. No arrests have been made."

Cristina, a former big game hunter, was a long-time opponent of Mozambique's ruling, Marxist Frelimo Party.

According to sources in the 600,000-member Portuguese community here, many of whom fled Mozambique and Angola after independence, he was an agent of the former Portuguese secret police, PIDE, and tried unsuccessfully to infiltrate the Frelimo movement in 1964.

After the revolution in Portugal in 1974, which precipitated independence for the Portuguese colonies, Cristina fled to Rhodesia, where the sources say he worked with the Rhodesian Central Intelligence Agency in forming the Mozambique National Resistance Movement, mainly from black members of the Portuguese Special Forces who had fought against the black African nationalist movements in the colonies.

The Mozambique government of President Samora Machel has claimed that after Zimbabwean independence, Cristina crossed into South Africa with a group of his guerrillas and continued operating from there with South African assistance.

The Mozambican rebels have been expanding their operations in recent months and are now active over a wide area north of the capital, Maputo, and in the vicinity of the port of Beira.

They have made several sabotage attacks on the port and on the railroad to Zimbabwe. Beira is Zimbabwe's main outlet to the sea.

They also have sabotaged Zimbabwe's Feruka oil refinery and the oil pipeline to Harare, the Zimbabwean capital.

These attacks have caused several acute fuel shortages in Zimbabwe, aggravated for a time by the simultaneous withdrawal by South Africa of locomotives that had been lent to Zimbabwe before independence.