The government has ordered a wide-ranging probe into the South African Council of Churches following allegations of financial irregularities within that group.

The investigation, ordered last month by Prime Minster Pieter W. Botha, could lead to restrictions on receiving money from overseas churches, which now provide the bulk of the council's funds. The council is a champion of black grievances against apartheid under the leadership of black Anglican Bishop Desmond Tutu.

The irregularities, which were brought to the attention of council officials by its former ombudsman and internal auditors, appear to involve sloppy bookkeeping, misjudgments, mismanagement and the questionable use of some unaudited funds, rather than theft or fraud.

But the scope of the government's investigation by a Botha-appointed panel lends support to the widespread belief that its purpose is not only to examine these financial problems, but also to discredit the council, which officials from Botha on down have accused of subversion.

The panel has been asked to examine "the inception, development, objects, history and activities" of the council as well as the "organizations and people connected with giving such money or assets to" the council.

Church bodies are exempt from legislation that requires fund-raising organizations to get a license from the state. Legal observers say that if the panel's recommendations require it, the government could amend the legislation or take a stricter interpretation of it in order to reduce funds going to the council.

If so, it would not be the first time the government has acted against the council. In 1979 it secretly provided more than $350,000 to a right-wing Christian group that was to run a covert campaign against the council in an attempt to break its influence among English-speaking churches. The effort, exposed by newspapers, had little effect.

The government has been angered by the council's payments for the legal defense of political defendants, its support for civil disobedience of discriminatory laws and its encouragement of conscientious objectors to military service.

Police Minister Louis Le Grange once assailed the council, which represents 15 million, mostly black, Christians through its affiliated churches, for "giving whites a guilty conscience."

The council has also given money to squatters for food and bail, helped pay for post-mortems on people who died in police custody and supported families of political detainees.

Tutu's predecessor, John Rees, has also said without elaboration that some funds were used in "sensitive areas." Some observers believe that money may have been used to help young black activist students during the tumultuous years of 1976-1977 in projects that were not violent or subversive, but in which the government is now seeking to expose the council's role.

However, some recent disclosures about the council's disbursements have shown its own officials profitting from the funds they administer, revelations which have elicited criticism even from the council's supporters.

For example, Tutu admitted in a related court case in October that he received about $15,000 in 1978 from the council to help buy his own home in Soweto. At the time, he had been named as the next secretary general of the council but had not yet taken up the post. Rees gave him the sum, telling Tutu it was an anonymous gift.

In the same court case, it was also disclosed that a council vice president, Sally Motlana, and her husband, Nthato Motlana, received a stipend of $7,000 after spending several months in detention in 1977.

In a recent interview, Tutu justified the money for his house as a gift as one any large organization would give a top employe. He said the contribution to the Motlanas was just compensation for their financial losses while in jail. Motlana is a physician and his wife a shop owner. Both are community leaders in Soweto.

Most released detainees who receive money from the council get much less than what the Motlanas received. The stipend is usually $50 or $100.

Tutu charged the special inquiry into the council was "a political ploy."

"They have been gunning for the council, gunning for me, and they would latch onto any excuse with considerable alacrity," the bishop said. "If we weren't doing the things we are doing, if we did not upset the government and upset the whites, they wouldn't give two hoots" about the irregularities.

He pointed out that the final report of outside auditors whom the council called in had found "weaknesses" in its financial administration, but "that not at any time was it inadequate."

As for the unaudited funds, Tutu said the council had acted as a conduit for overseas funds to other groups and "our responsibility ended when the funds were transferred." Many of the recipients were "small, rural people, many illiterate," from whom it would have been "unrealistic" to expect financial reports, Tutu said.