A South African court today halted a leading newspaper from publishing incriminating allegations against members of Prime Minister Pieter W. Botha's Cabinet.

The order came amid growing concern that Botha will move in Parliament to block any further publication of unproven allegations -- a step that would put a severe restraint on South Africa's relatively free press.

The court-ordered censoring of the Rand Daily Mail, the major opposition newspaper, came at the request of Jimmy Kruger, South Africa's police and justice minister and a figure in the country's most serious crisis in years.

The censorship order came to late to prevent publication of the offending allegations in the paper's early editions, but later editions contained two large white spaces, where the material had been removed.

The censored allegations purported to tie the full Cabinet as well as President John Vorster to portions of a scandal involving misuse of government funds in propaganda activities, which is threatening to bring down Vorster's government.

Revelations about the scandal appearing in the press have shaken public confidence in the government, and there are growing indications Botha is hardening his stance on foreign policy issues to win support from hard-line elements in his Nationalist Party government.

The first casualty could well be the tortuous negotiations over the United Nations plan to bring independence ot Namiblia. The government last week rejected elements of the U.N. plan and staged bombing raids against Namibian guerrilla bases in Angola and Zambia.

The threats against press freedom also caused foreboding since just two years ago the government introduced legislation to severely censor the press. It withdrew the bill only after warning the press to discipline itself, and the government is hardly likely to regard the Information Ministry allegations as an example of such descipline.

In today's devolopment, the provincial-level Cape Supreme Court ordered the Mail to withhold publication of the three paragraphs containing the allegatins until a March 27 hearing when the paper is to tell the court why the publication ban should not be made permanent.

The deleted portions amplify allegations made in the Mail last week by Eschel Rhoodie, former information secretary, that one of the most confroversial activities now under scrutiny was discussed at Cabinet meetings and initiated with Vorster's approval.

A special government investigation last year found Rhoodie, former information minister Cornelius Mulder and South Africa's former intelligence agency chief, Hendrik Van den Bergh, the only officials responsible.

According to Rhoodie, one of the most spectacular of the controversial projects, the clandestine funding of a progovernment newspaper, The Citizen, with misappropriated government funds, was discussed at Cabinet meetings in 1977 and 1978 and begun with Vorster's approval.

This accusation by Rhoodie implies that the whole Cabinet shares responsibility for The Citizen project, which was condemned by the special government probe last December. Its final report described Vorster as shocked when he found out belatedly about The Citizen funding.

One censored section quoted Rhoodie on a conversation he allegedly has with Kruger in which the justice minister indicated that "this [The Citizen] could implicate the prime minister, who had warned us that he would have to resign if The Citizen story got out."

"I took it by 'us' he was referring to the Cabinet," Rhoodie went on.

In an uncensored companion story today, the Mail printed an account from Rhoodie naming six ministers in the present Cabinet, including the prime minister, who allegedly cooperated in or had knowledge of one or more of Rhoodie's secret projects. He accused Prime Minister Botha of being "in at the start of a major multimillion secret project in 1973" which is still continuing.

Rhoodie also claimed that Foreign Minister Pik Botha was asked by Mulder "to participate in a secret projject in the United States. Mr. Botha knows that he participated in this proect." No details were given.

Since the secret propaganda campaign became public last year, the government has sought to prevent disclosures about how it was run and what its projects consisted of, some of which reportedly could have political implications for South Africa and its friends in the United States.

From his self-imposed exile in Paris, Rhoodie has threatened to disclose details of those secret projects if the government does not clear his name.

In today's Mail story, he asserts that, "To say Dr. Mulder and I acted on our own, that we are the only ones responsible, is to slander my efforts to defend myself in public.

"What is there to fear on the part of Mr. Vorster, Mr. Botha, [Finance Minister] Owen Horwood and the other ministers to admit to their knowledge of secret projects and the financing thereof? After all, a great many operations are being continued with the new Cabinet's approval so that not everything we undertook can be labeled as amateurish,"

The government has described Rhoodie's disclosure threats as blackmail.