Cornelius P. Mulder, South Africa's minister of black affairs, resigned from his Cabinet position yesterday just as a high-level probe began into alleged misuse of secret government funds by the Department of Information, which Mulder, once headed.

Maintaining his innocence, Mulder said he had "no pangs of conscience." He was stepping down from his ministerial post, however to assist Prime Minister Piter W. Botha [WORD ILLEGIBLE] "in repulsing this on slaught against the National Party, the government and the country," Mulder said.

Strong reaction has followed revelations that millions of taxpayers' dollars, secretly allocated to the Department of Information, and meant to improve South Africa's image abroad, were used instead of secretly set up a pro-government newspaper here as well as finance such projects as the making of an commercial adventure film.

Meanwhile Prime Minister Botha announced unexpectedly last night that he was relieveing Judge Anton Mostert, who last week defied Botha by releasing sworn testimony containing the charges of abuse, from his duties as a one-man commission investigating violations of currency exchange controls. Moster was ordered to turn over all his documents to a three-man commission Botha appointed last week to investigate the allegations.

The prime minister's action is certain to stir renewed charges that he is trying to cover up the full extent of the scandal. The newly appointed commision is to hear all its evidence in private.

Not a man to give up power easily, Mulder apparently responded to pressures within the ruling National Party for a full accounting and assignment of responsibility for the worst political scandal in its 30 years in power.

Within the party, Mulder's resignation is expected to affect the chafing relationship between the moderate faction, led by Foreign Minister Roelof "Pik" Botha and the hardline wing in which Mulder was the principal figure. The moderates will undoubtedly view Mulder's stepping down as an opportunity to erode the strength of the hardline faction, which seemed to have tightened its grip on the party in recent months.

In addition, Mulder's vacating of the important post of black affairs minister, to which he was appointed in February by former prime minister John Vorster, of fers Prime Minister Botha a chance to give the first broad indication of how he intends to deal with the country's most crucial problem - the growing political aspirations of the black majority.

The appointment of a moderate could be a weathervane for Botha's intentions.

In June, Mulder was relieved of his responsibility for the Information Department, which was transfereed to Pik Botha as part of the Ministry of Foreign Affairs.

Mulder, who narrowly missed becoming prime minister in a party vote less than six weeks ago, will retain his seat in parliament and his powerful position in the party hierarchy as leader of the transvaal Province delegation. Thus Mulder could make a political comeback up by protestations of innocence are backe up by the findings of the investigating commitee.

That committee, headed by an Oxfordeducated supreme court judge, Rudolph Erasmus, is expected to have its report ready for a special-parliamentary session called for Dec. 7.

Mulder has agreed to testify before the commission. Yesterday he said: "I am convinced of my innocence and therefore I am still prepared to give evidence before the Erasmus commission to prove my honesty and integrity beyond all doubt." Mulder said everything he had done was done "in the conviction that I was serving my country."

However, Mulder is expected to face tough questioning from the opposition in parliament about whether he deliberately misled that body when asked earlier this year whether the government was putting money into the Citizen, a pro-government newspaper. At that time, Mulder said "The Department of Information and the government do not give funds to the Citizen."

Some informed political observers here believe that the full scope of the scandal has not been revealed and that the full consequences for the white minority government, dominated by the National Party with more than three-quarters of the seats in parliament, are not yet clearly foreseen.

Press reports in Afrikaans-language newspapers have again suggested that there is a link between the former Department of Information and the slaying almost a year ago of a prominent National Party member, Robert Smit. He and his wife were killed in their home and the police have never solved the crime.

Smit was an economist who had represented South Africa on the International Monetary Fund. There is speculation that he came across a currency smuggling scheme connected to the Information Department and was killed to prevent disclosure.

The authorities denied there was any such link when the papers first made this suggestion a few months ago but the fact that it now reappears in an Afrikaans newspaper is regarded here as significant.

There have also recently been death threats to former Information Department officials and gunshots have been fired at the home of a journalist.

There are also questions about how much Prime Minister Botha, then minister of defense, and Vorster, knew about the abuses of the secret fund and about whether allegations that the country's highest intelligence officer, Gen. Hendrik van den Bergh, tried to cover up the scandal, are true.