South African Prime Minister P.W. Botha has criticized the Reagan administration, saying its recent policy statement on apartheid unfairly singled out South Africa for reproach and was based on a "central misconception" of politics in that white-ruled nation.

In remarks reported yesterday in Cape Town, Botha replied to a speech last week by Undersecretary of State Lawrence Eagleburger, saying, "The South African government would like to know why his concern for democratic practices stops short at South Africa's borders."

The prime minister, citing what he described as repressive measures in neighboring Angola, Mozambique and Lesotho, asked, "Can the U.S. indicate in which of these states there is a free press, a free political process and respect for private property rights? Why was the U.S. not objective and why did it imply, by criticizing South Africa, that what happened in these other states was acceptable?"

Botha's statement to the Parliament was the first official response to Eagleburger's speech, which gave the most detailed description to date of U.S. policy goals in southern Africa and branded as "morally wrong" race segregation in South Africa. The speech was widely seen here as an effort to quell criticism on Capitol Hill and among civil rights groups that the administration's policy is too favorable to South Africa.

Botha accused Eagleburger of attempting to "dictate" to South Africa how blacks, who make up 70 percent of the population but have no representation in Parliament, should be governed there. Eagleburger had strongly condemned the South African policy of establishing separate black states or "homelands," which the United States has refused to recognize.

"The central misconception in Mr. Eagleburger's speech was that South Africa was a unitary state containing a single South African nation with a 'black majority' and a 'white minority,' " Botha said.

He denied that he had a "secret agenda" for reform in South Africa, a reference to Eagleburger's statement that Americans should not expect "South Africa's would-be reformers to announce their game plan and their bottom line to the world at large."

A State Department official downplayed the significance of Botha's remarks, suggesting that the prime minister's criticism was aimed mostly at placating domestic political foes who oppose the government's plan to grant some political rights to persons of mixed blood and Indian descent.

"Just like we have to speak to our audience, he has to speak to his, and we'll have to agree to disagree with respect to apartheid," the official said.

But Rep. Stephen J. Solarz (D-N.Y.), a critic of U.S. policy in Africa, said Botha's speech "shows the South African government has no intention of fundamentally changing the apartheid system and that the administration is naive to think otherwise."

Solarz has sponsored one of several amendments approved by House committees that would limit economic ties to South Africa.

His amendment would restrict U.S. bank loans to South Africa, force U.S. companies doing business there to comply with an antidiscrimination code and ban the sale of South African gold coins here. It is likely to be debated on the House floor later this month.