South Africa's worsening political scandal over the misuse of government funds by top officials is weakening the credibility of Prime Minister Pieter W. Botha and threatening his six-month-old administration.

Former Information Department secretary Eschel Rhoodie charged this week that Botha and other Cabinet members were briefed on the secret financing of a progovernment newspaper with misappropriated funds and that the current finance minister was involved with the funding of the paper.

Botha and his top aides have denied the charges.

Rhoodie, who was named as one of those responsible for the scandal by an investigative team appointed by Botha, revealed his charges in an interview with the Rand Daily Mail newspaper.

The new challenge to the prime minister comes at a time when public confidence in the government already has been severely shaken -- particularly among the country's Afrikaners, the Dutch-descended whites who dominate the minority regime's ruling party.

Rhoodie's allegations also implicate former prime minister John Vorster, South Africa's leading politician who headed the government for 12 years. If charges that he approved many of Rhoodie's clandestine projects are substantiated, Vorster most likely will be forced to step down from the largely ceremonial post of president.

The government report last December exonerated Vorster of any responsibility in the scandal, instead placing the blame for the newspaper-funding scheme on Rhoodie, former information minister Cornelius Mulder and the former head of intelligence, Gen. Hendrik Van den Bergh.

Rhoodie's countercharges appear to be part of an attempt to defend himself against the government report and deflect the blame to his accusers. His charges cast doubt on the investigative team's conclusions and raised suspicions of a coverup that had Botha's approval. The former information secretary has offered no documentation of his allegations except to call for the release of all the evidence heard by the investigators.

At the apparent behest of the government, the probers have refused thus far to release that evidence.

The publication Friday and Saturday of Rhoodie's story follows several weeks during which Rhoodie, who is in a self-imposed exile that has taken him to Ecuador, Italy, Britain and France, has threatened to reveal details of numerous secret South African projects.

In a curious development, Van den Bergh flew to Paris early last week to meet Rhoodie, where they reportedly struck a deal in which Rhoodie agreed not to reveal details of the secret project because it would not be in South Africa's best interests.

Under the reported deal, Rhoodie was guaranteed a job in an unnamed foreign country with a South African company. This has aroused suspicion here that either the Botha government, Van den Bergh or someone else in South Africa is trying to buy Rhoodie's silence.

If Botha is forced to call an election because of the "information scandal," as it is called here, there is little chance that the ruling National Party would be voted out of office. It holds three-quarters of the seats in parliament. There are well-founded fears, however, that a very conservative faction in the party, led by Andries Treurnicht, would emerge with considerably more strength than it has now.

Treurnicht has not been implicated in the scandal and has aspirations to become the party leader and therefore prime minister. His conservative policies would probably exacerbate the difficulties in finding a solution to the country's racial problems.

The new pressure on the Botha government comes at a bad time for Western efforts to get a negotiated settlement to the armed conflict in Namibia, the territory South Africa has administered as Southwest Africa since 1920.

If Rhoodie's charges are proved, it would mean that most of Botha's Cabinet must have known the truth when former information minister Mulder told Parliament last May that no government money had gone to finance the Citizen, Rhoodie's progovernment newspaper whose aim was to counter South Africa's negative image.

Botha, then the defense minister, has admitted that he allowed money from his budget to be transferred to the Information Department for secret projects launched to counter anti-South African publicity at home and abroad. But Botha, who became prime minister last September, has denied he knew exactly what the projects were.

It is also believed that money from the defense budget paid the loan to Michigan publisher John McGoff to finance an unsuccessful attempt to purchase The Washington Star. Botha's investigators reportedly are looking into this connection.

Rhoodie also alleged that Finance Minister Owen Horwood was involved with the funding of the Citizen from its inception. Horwood is a holdover from Vorster's Cabinet, as are most of Botha's ministers.

Last month Botha, harassed by opposition queries on the Information Department scandal, pledged to "resign and call an election" if it could be proved that any of his Cabinet or himself "knew who had authorized the irregular use of state money" or "knew about the subsidies which the Citizen had received from the state."

The Citizen cost unknowing South African taxpayers more than $36 million.

Botha today reacted violently to Rhoodie's story, saying he rejected "these repeated smear stories with contempt."

"Dr. Rhoodie's contemptible behavior from overseas to connive with certain opposition newspapers is a transparent game to take vengeance on people who exposed his irregularities." Botha said.

The irony of Rhoodie making his revelations to the Mail has not escaped most observers -- Rhoodie set up the Citizen to counter the influence of the moderate Mail.