The Reagan administration, seeking to counter criticism that it is too closely aligned to South Africa, yesterday defended its policy in a statement that characterized South Africa's political system as "morally wrong" and rejected "the legal and political premises and consequences of apartheid."

In what State Department officials described as a "major policy speech," Lawrence S. Eagleburger, undersecretary for political affairs, acknowledged that administration policy "has occasioned controversy," and added, "Some, it appears, have misunderstood the message or chosen for their own reasons to misunderstand it."

Eagleburger, in remarks prepared for delivery last night to the National Conference of Editorial Writers in San Francisco, made a lengthy defense of the administration's controversial efforts to improve relations with South Africa and to link independence for Namibia with agreement for withdrawal of Cuban troops from Angola.

His remarks were a restatement of existing policy and showed no sign that the administration might be shifting course.

But Eagleburger put them in a context aimed at deflecting charges from congressional liberals and civil rights groups that the administration has not been evenhanded in balancing its ties with South Africa against black African aspirations.

A senior State Department official, who asked not to be identified, said, "The speech was intended as a corrective for misapprehensions about what our policy really is. We feel the administration has been attacked unfairly for being too soft and offering too many carrots to South Africa. That's a misconception that we want to set straight."

To that end, Eagleburger put special stress on criticizing apartheid, including such features of the system as the attempt to segregate the black majority tribal homelands and repression of dissent through measures "like banning and detention without due process of law."

"By one means or another, South Africa's domestic racial system will be changed," he asserted. "Our policy is directed, therefore, not at whether a non-racial order is in South Africa's future or what the shape of that non-racial order will be, but how that non-racial order will be arrived at." He said that U.S. policy aims at encouraging change through peaceful means, and he rejected, as "measures that rest on no discernible philosophic or policy premise," calls for economic boycotts or pressures on U.S. firms not to invest in South Africa.

"This apparent quest for symbolic disassociation is, in reality, a formula guaranteed to assure America's irrelevance to South Africa's future," he said.

On the related regional issues of Namibian independence and the Cuban presence in Angola, Eagleburger essentially repeated the message delivered by Secretary of State George P. Shultz in a May 26 meeting with black African leaders at the United Nations.

Eagleburger said, in effect, that the two issues are linked implicitly because the presence of Cuban troops in Angola has made South Africa fearful of relinquishing its control over Namibia and that the impasse is unlikely to be broken unless a way is found to alleviate South Africa's security concerns.