South Africa has announced that it again will choke the flow of traffic between its borders and landlocked Lesotho in a political reprisal against the little African kingdom with which relations are deteriorating.

Announcing the crackdown, the second time it has tightened border controls in the past two months, Foreign Minister R. F. (Pik) Botha said in Pretoria last night that strict control procedures would be applied at all the border posts in retaliation for the arrest and alleged maltreatment of a low-ranking South African policeman who went to Lesotho to coach a soccer team.

Botha also said the move follows the arrest Monday of a member of Lesotho's Para-Military Force who was found on the South African side of the border with a concealed automatic rifle Monday. Both actions leave South Africa with "no alternative" but to apply the stricter border controls, he said.

People who crossed the main border post at Caledon Bridge today said the slowdown had not started yet.

South Africa initiated the crossing slowdowns--holding up vital supplies to Lesotho and causing massive traffic jams--in May after two terrorist bombings in the South African cities of Pretoria and Bloemfontein.

South Africa said the thorough searches were a security precaution, but government sources in Pretoria admitted privately that it was really to drive home South Africa's complaint that insurgents of the underground African National Congress operate out of Lesotho. Officials there deny the charge.

The slowdown quickly demonstrated what an economic hold South Africa has over Lesotho and other neighboring black states, and how this, as well as its superior military strength, can be used as a weapon should they displease Pretoria.

Within days, distress signals were going up as Maseru, the capital of Lesotho, began to run out of fresh food, including milk and vegetables, and as workers who commute across the border were delayed.

After a fortnight Lesotho's foreign minister, Evaristus Sekhonyana, met Botha here and the slowdown ended. Stricter rules for African National Congress refugees in Lesotho ensued.

Observers said that South Africa's willingness to repeat the squeeze over a much lesser issue is an indication of deteriorating relations between the two countries. Ties began to founder when South Africa conducted a raid on residences allegedly used by congress members in Maseru in December.

Since then, Lesotho's prime minister, Chief Leabua Jonathan, who once enjoyed warm relations with South Africa, has made an extensive tour of communist countries and is in the process of setting up embassies with the Soviet Union. South Africa sees this in a sinister light, since it believes itself to be the target of a "total onslaught" directed from Moscow.

In explaining the reasons for the renewed slowdown, Botha said that the South African policeman, Warrant Officer D. T. Sello, had gone to Lesotho June 11 at the invitation of a team in Mafeteng.

He was arrested, Botha said, adding that it had taken a month before Lesotho responded to his department's inquiries about Sello.

In a separate incident that observers see as further evidence of the tense relations between South Africa and its black neighbors, Mozambique announced last night that it is to put on trial six passengers of a South African light plane that made an unscheduled landing there on a flight from the Indian Ocean Comoro Islands three weeks ago.

The six passengers--two each from South Africa, Britain and France--say they were running short of fuel, but Mozambique says an examination of the plane showed it still had adequate fuel.

Sources in Maputo point out that the incident should be seen in the light of nervousness following a reprisal air raid by South Africa on a suburb of the Mozambican capital after the Pretoria bombing in May.

South Africa claimed the raid was directed at congress insurgents, but Mozambique denied any insurgents were there.