For the second time in less than five weeks, the Angolan government has accused South African forces of attacking targets not directly associated with anti-South African guerrillas stationed in Angola.

Both the Angolan ambassador in Belgium and the state-run Angolan radio charged today that airborne South African commandos killed 20 people, including 18 civilians, when they blew up transport facilities during raids Sunday on three major Angolan towns. On Sept. 26, the Angolans said South African Mirage jet fighters bombed housing and industrial quaters in two towns, killing more than 50 people.

South African officials, as is customary, would not explicity deny or confirm the latest reports. Since Angolan authorities do not allow journalists to visit areas allegedly attacked, the charges usually are impossible to verify.

The latest charge follows a claim Oct. 23 by the president of another neighboring state, Kenneth Kaunda of Zambia, that 400 South African troops had invaded his country. He did not state what they did there. Both Angola and Zambia offer sanctuary to guerrillas of the black nationalist Southwest African People's Organization (SWAPO), which is fighting South African troops in the territory of Namibia (Southwest Africa).

The Angolan claims come at the same time that Zimbabew-Rhodesian government troops have stepped up their attacks on civilian and economic targets in Zambia and Mozambique in their fight against guerrillas attemping to topple the government in Salisbury.

South Africa and Zimbabwe-Rhodesia have cooperated closely on military matters, espcially since Pieter W. Botha became prime minister in South Africa last year.

The most spectacular example of this escalated campaign of non-guerrilla targets by the Zambabwe-Rhodesian forces was the destruction in mid-October of two bridges linking Zambia to Tanzania. They were conduits for about 30 percent of Zambia's trade.

In Mozambique, the Defense Ministry disclosed the destruction of three railway bridges earlier this month. Civilians and local government officials have told recent visitors in Mozambique of other attacks on such civilian targets as shops, dams and road bridges by the Salisbury forces.

These attacks are intended to disrupt the local economy and dampen the support of the civilian population for the guerrilla groups, according to most analysts.But some observers note that the railways may have been targets in both countries to halt arms shipments to the guerrillas.

This could also explain the alleged attacks against Angola railway and highway facilities. A communique from the Politburo of Angola's Marxist ruling party stated that 150 South African commandos, transported in 11 helicopters, destroyed a railway tunnel and mined railway lines near the towns of Lubango, the capital of Angola's southern district, and the ports of Mocamedes and Porto-Alexandre Sunday.

The communique, read on Angolan radio and monitored here by the government-run radio, also reported that four highway bridges on the road between Lubango and Mocamedes were blown up. The targets are more than 100 miles inside Angola.

Arms shipments for SWAPO, which is backed by the Soviet Union, are thought to enter Angola through these ports. They would then be shipped to Lubango on the way to the guerrilla bases in southern Angola.

The Angolans did not specify how the 18 civilians and two Angolan soldiers died.

A spokesman in Pretoria said South Africa was not seeking confrontation with neighboring states.

"We are merely in the north of Southwest Africa to protect the local population against atrocities by SWAPO terrorists, and it was also stated previously that we maintain the right to follow these terrorists to their hiding places no matter where they are," he said.

Commenting on the Angolan accusations, Foreign Minister Pik Botha said. "It is a smokescreen they are using for tactical reasons. The basic cause of the conflict is the attacks the terrorists are launching on Southwest Africa.

"Basically, Angola is harboring terrorists who use Angola as a springboard for terrorist attacks against Southwest Africa," Botha said.

In the past week, SWAPO guerrillas abducted a group of children from their school in northern Namibia, according to the South African military. Yesterday, it was reported that a local black official and his bodyguard were killed by the guerrillas.

A United Nations plan for a cease-fire and a peaceful transition to independence in Namibia is bogged down in discussions about its implementation.