The leaders of five major South African churches told President Pieter W. Botha today that the country's political crisis would not end until his government took significant steps to abolish apartheid and ended the current state of emergency. They came away apparently finding little hope that change was likely.

Denis Hurley, the Catholic archbishop of Durban, told a press conference after the meeting that "our two perceptions of South Africa were so different that we hardly began to communicate at all." He said the president "did not really answer any of the issues we raised. We haven't anything substantial to take with us as a result of this meeting."

Meeting with Botha in the capital of Pretoria, members of the nine-man delegation said they told him the policies of his white-minority government were primarily to blame for the black turmoil that has gripped this nation for a year and resulted in more than 600 deaths.

Earlier this morning, Moral Majority leader Jerry Falwell delivered a far different message after meeting with Botha, expressing strong support for the South African government. He said he would launch a million-dollar "reverse campaign" in the United States to convince the Senate not to give final approval next month to legislation authorizing economic sanctions against Pretoria.

The meetings took place on a day when police reported yet another black man killed and a black policeman injured. They also reported 64 more persons had been arrested, bringing to 2,024 the arrests since the emergency decree took effect July 21. Of these, 922 are still being held.

Conspicuous by his absence from today's meeting was Nobel Peace laureate Desmond Tutu, the Anglican bishop of Johannesburg, who bowed out last night to protest Botha's hard-line policy speech last Thursday in the port city of Durban. That speech appeared to rule out most of the steps the church leaders called for today.

Tutu asked for a meeting with Botha a week after announcement of the state of emergency. Botha said then that the bishop might accompany the delegation of prelates scheduled for today. The president underlined that Tutu should first disavow his stance favoring tactics of civil disobedience.

Botha's session with the delegation reflected the hardening lines and wide gap between the position of the white government and that of even its most nonviolent liberal critics.

Led by Philip Russell, the Anglican archbishop of Cape Town, the delegation presented Botha with a memorandum calling for four immediate steps: a declaration of intention to dismantle apartheid, a call for a national constitutional convention, the opening of talks with all recognized black leaders and the lifting of the emergency decree.

"We are utterly convinced that unless people see a significant substantial move from apartheid to sharing, there will be no end to the unrest," said the statement of the delegation, which also included Methodist, Congregational and Presbyterian leaders. Four of the nine are white, four black and one of mixed race.

The memorandum accused South African security forces of widely abusing the broad emergency powers they were granted four weeks ago to stamp out unrest.

In a brief statement later today, Botha said he had ordered his minister of justice to investigate "a few allegations" of police misconduct. He described today's talks as "frank" and pledged "further talks will follow."

Last Thursday, Botha rejected calls that he issue a statement of intent, and also refused to release imprisoned black nationalist Nelson Mandela -- one of those leaders who many black spokesmen say would have to be present for any future negotiation to be considered legitimate. Botha also said he would only lift the emergency when political violence had significantly declined.

While Archbishop Russell said he was "not without hope" that the meeting would have some impact on changing Botha's views, other members of the delegation were more pessimistic.

"There are two South Africas and there are two clocks running in South Africa, the one at past midnight and the other at long before," said the Rev. Peter Storey, leader of the country's Methodist Church. "We were trying to represent those for whom midnight has already struck . . . the South Africa where hopelessness and despair have given way to rage."

Falwell, the Baptist minister winding up what he called a "fact-finding" trip here, described a far different South Africa after his session with Botha. "Apartheid is not the policy of the government, but it is a social reality," Falwell told a press conference. "Reform is the policy of the government."

Falwell said the government was "making progress" but that Botha had to be move cautiously to avoid white backlash. "If people to the right of the president sit where he sits, they will abolish the reforms and do things that are much worse," he said. "When these people are driven to the wall, they will fight back."

The Moral Majority leader, who operates the conservative coalition from his Lynchburg, Va., headquarters, said he would encourage his members to buy gold Krugerrands, invest in companies that do business in South Africa and lobby their senators to defeat the sanctions bill when the Senate returns next month. The House of Representatives has already approved the measure as resolved from House and Senate versions by a conference committee. It enjoys widespread bipartisan support.

Blaming the news media for not telling "the true story of South Africa," Falwell said his group would spend $1 million to produce two one-hour television specials to be shown on Christian broadcasting networks in the United States on the next two Sundays.

"There are millions of Americans who do not agree with what Bishop Tutu is saying and with what others have been saying in the American media," said Falwell, who said he would encourage President Reagan to veto any sanctions bill that came before him.

Methodist leader Storey retorted later, "I don't think Mr. Falwell has done a service to the people of South Africa. His perception is totally inaccurate and he doesn't know what is happening in the lives and experiences of the people."

Police confirmed tonight they had used shotgun rounds and rubber bullets to disperse a mob of black youths in the township of Duncan Village outside East London yesterday.

Witnesses cited in an East London newspaper today said at least 25 persons were injured when shots were fired on a group holding a church service at the home of an earlier shooting victim in the township, where at least six people have been killed in the past week. Police said the shots were fired at youths in an illegal demonstration.

A 24-year-old man and 13-year-old boy were flown to a Cape Town hospital from East London today with serious gunshot wounds in their backs, the South African Press Association reported tonight.